Plugin compatibility between Pymol on Windows and Gromacs on Windows 10 WSL

[ggotthar]

Hello,

The last Windows 10 creators update has enabled the possibility use bash / linux system on windows. I have probe the possibility to use your dynamics plugin on a windows compiled pymol and a debian WSL compiled gromacs. Interestingly, with only few adaption, I was able to install the plugin on the Windows Pymol. The first one was to adapt the file system checking for directory creation:

from os.path import expanduser

def setGromacsDynamicsAndProjectDirs(): global project_name, dynamics_dir, project_dir

project_name = "nothing"

homeDir = expanduser("~")

gmxHomeDirPath = os.path.abspath(homeDir)
dynamics_dir = os.path.join(gmxHomeDirPath, '.dynamics', '')
project_dir = os.path.join(dynamics_dir, project_name, '')`

Default folders are then created.

The second step is to allow the script to start executables through the WSL bash. To do this, a simple way is to call "bash -lic '" + command + " '" when the script start a command. With this, it's starting the command, but the parameters are not injected.

So, I was wondering if you have a good solution to pipe command and parameters for the job (result in stdin: is not a tty). I feel it should not be too complex but I don't have enough experience in coding to find a solution. If you have any idea, I would be very interested. Many thanks, All the best,

G.

Below is the modified plugin code.

#!/usr/bin/env python2
#-*- coding: utf-8 -*-

##This software (including its Debian packaging) is available to you under the terms of the GPL-3, see "/usr/share/common-lic enses/GPL-3".
##Software is created and maintained by Laboratory of Biomolecular Systems Simulation at University of Gdansk.
##Contributors:
##- Tomasz Makarewicz (btchtm@ug.edu.pl)
##- Ajit B. Datta (ajit@jcbose.ac.in)
##- Sara Boch Kminikowska
##- Manish Sud (msud@san.rr.com; URL: www.MayaChemTools.org)
##

##Plugin Version
plugin_ver = " 2.2.0pre"

##--Import libraries--
##Import nativ python libraries
import subprocess, time, os, shutil, thread, pickle, Queue, re
##Import libraries for tk graphic interface
from Tkinter import *
from ttk import Progressbar, Scrollbar
import tkSimpleDialog, tkMessageBox, tkFileDialog, Pmw
##Import libraries from PyMOL specific work.
from pymol import cmd, stored, cgo
from os.path import expanduser

##Check for ProDy
try:
    import prody
    prody_true = 1
except:
    prody_true = 0

##This class is responsible for interface to GROMACS. It will read all important data from GROMACS tools.
class Gromacs_output:

    version = "GROMACS not found"
    command = ""
    force_list = []
    water_list = []
    group_list = []
    restraints = []
    plumed_true = 1

    def __init__(self):
        global status
        #Remove garbage
        garbage_files = next(os.walk(dynamics_dir))[2]
        for garbage in garbage_files:
            if garbage[0] == "#":
                os.remove(dynamics_dir+garbage)
        status = ["ok", ""]

        global gmxExe, gmxVersion
        self.version =  gmxVersion
        self.command =  gmxExe

        # Track current directory and switch to dynamics_dir before invoking gmx...
        current_dir = os.getcwd()
        os.chdir(dynamics_dir)

        self.init2()
        self.detect_plumed()

        # Switch back to current directory...
        os.chdir(current_dir)

    def init2(self):
        print "Reading available force fields and water models"

        fo = open("test_gromacs.pdb", "wb")
        fo.write("ATOM      1  N   LYS     1      24.966  -0.646  22.314  1.00 32.74      1SRN  99\n");
        fo.close()

        gmxStdinFilePath = "gromacs_stdin.txt"
        fo = open(gmxStdinFilePath, "w")
        fo.write( "1\n");
        fo.write( "1");
        fo.close()

        gmxStdoutFilePath = "test_gromacs.txt"

        cmd = self.command + " pdb2gmx -f test_gromacs.pdb -o test_gromacs.gro -p test_gromacs.top"
        executeSubprocess(cmd,  gmxStdinFilePath, gmxStdoutFilePath)
        lista_gromacs = readTextLines(gmxStdoutFilePath)

        #Reading available force fields
        force_start_line = 0
        while lista_gromacs[force_start_line] != "Select the Force Field:\n":
            force_start_line = force_start_line + 1
        force_start_line = force_start_line + 2
        force_end_line = force_start_line
        while lista_gromacs[force_end_line] != "\n":
            force_end_line = force_end_line + 1
        force_list = lista_gromacs[force_start_line:force_end_line]
        force_list2 = []
        number = 1
        for force in force_list:
            force_list2.append([number, force[:-1]])
            number = number + 1

        self.force_list = force_list2

        #Reading available water models
        self.water_list = getWaterModelsInfo(lista_gromacs)

        print "Reading available groups"

        gmxStdinFilePath = "gromacs_stdin.txt"
        fo = open(gmxStdinFilePath, "w")
        fo.write( "1");
        fo.close()

        gmxStdoutFilePath = "test_gromacs.txt"

        cmd = self.command + " trjconv -f  test_gromacs.pdb -s test_gromacs.pdb -o test_gromacs2.pdb"
        executeSubprocess(cmd,  gmxStdinFilePath, gmxStdoutFilePath)

        group_test_list = readTextLines(gmxStdoutFilePath)

        #Reading available groups
        group_start_line = 0
        while group_test_list[group_start_line] != "Will write pdb: Protein data bank file\n":
            group_start_line = group_start_line + 1
        group_start_line = group_start_line + 1
        group_end_line = group_start_line + 1
        while group_test_list[group_end_line][0:14] != "Select a group":
            group_end_line = group_end_line + 1
        group_list = group_test_list[group_start_line:group_end_line]
        group_list2 = []
        number = 0
        for group in group_list:
            group1 = group.split(' has')
            group2 = group1[0].split('Group     ')
            if len(group2) == 2:
                group_list2.append([number, group2[1]])
                number = number + 1

        self.group_list = group_list2

    ##This function will update water list if force field is changed.
    def water_update(self, force_number):
        # Track current directiry and switch to dynamics_dir before invoking gmx...
        current_dir = os.getcwd()
        os.chdir(dynamics_dir)

        print "Updating available water models"
        gmxStdinFilePath = "gromacs_stdin.txt"
        fo = open(gmxStdinFilePath, "w")
        fo.write( "%d\n" % force_number);
        fo.write( "1");
        fo.close()

        gmxStdoutFilePath = "test_gromacs.txt"

        cmd =self.command + " pdb2gmx -f  test_gromacs.pdb -o test_gromacs.gro -p test_gromacs.top"
        executeSubprocess(cmd,  gmxStdinFilePath, gmxStdoutFilePath)

        lista_gromacs = readTextLines(gmxStdoutFilePath)
        self.water_list = getWaterModelsInfo(lista_gromacs)

        # Switch back to current directory...
        os.chdir(current_dir)

        save_options()
        return self.water_list

    ##This function will determine if PLUMED is compiled into GROMACS
    def detect_plumed(self):
        print "Searching for PLUMED integrated with GROMACS"
        gmxStdoutFilePath = "test_plumed.txt"
        cmd = self.command + " mdrun -plumed"
        executeSubprocess(cmd,  None, gmxStdoutFilePath)

        plumed_list = readTextLines(gmxStdoutFilePath)
        for line in plumed_list:
            if line[0:7] == "-plumed" or re.search("Unknown command-line option -plumed", line, re.I):
                self.plumed_true = 0
                break
        if self.plumed_true == 0:
            print "GROMACS does not appear to have PLUMED (disabling)"
        else:
            print "GROMACS detected with PLUMED (enabling)"

    ##This function will read atoms group for restraints for current molecule.  
    def restraints_index(self):
        self.restraints = []
        os.chdir(project_dir)

        fo = open("gromacs_stdin.txt", "w")
        fo.write( "q")
        fo.close()

        cmd = self.command+" make_ndx -f "+project_name+".pdb -o index.ndx"
        executeSubprocess(cmd,  "gromacs_stdin.txt", "restraints.log")

        index_list = readTextLines("restraints.log")

        index_position = 0
        atoms = ""
        for line in index_list:
            if line[0] == "[":
                self.restraints.append([])
                self.restraints[index_position].append(line)
                if index_position != 0:
                    self.restraints[index_position-1].append(atoms)
                index_position = index_position + 1
                atoms = ""
            else:
                atoms = atoms + line
        self.restraints[index_position-1].append(atoms)

##This class is responsible for performing molecular dynamics simulation with GROMACS tools.
class Gromacs_input:

    force = 1
    water = 1
    group = 1
    box_type = "triclinic"
    explicit = 1
    #variable to choose heavy hydrogen
    hydro = "noheavyh"
    box_distance = "0.8"
    box_density = "1000"
    restraints_nr = 1
    #four variables salt, positive, negative and neutral
    neutrality = "neutral"      
    salt_conc = "0.15"
    positive_ion = "NA"
    negative_ion = "CL"
    command_distinction = "\n!************************!\n"

    ##This function will change given variabless stored by the class (needed for lambda statements)
    def update(self, gmx_options, root=""):
        #Close mother window if present
        try:
            root.destroy()
        except:
            pass

        for key, value in gmx_options.items():
            if key == "force":
                self.force = value
            elif key == "water":
                self.water = value
            elif key == "group":
                self.group = value
            elif key == "box_type":
                self.box_type = value
            elif key == "hydro":
                self.hydro = value  
            elif key == "box_distance":
                self.box_distance = value
            elif key == "box_density":
                self.box_density = value
            elif key == "restraints_nr":
                self.restraints_nr = value
            elif key == "neutrality":
                self.neutrality = value
            elif key == "salt_conc":
                self.salt_conc = value
            elif key == "positive_ion":
                self.positive_ion = value
            elif key == "negative_ion":
                self.negative_ion = value
            elif key == "explicit":
                self.explicit = value
        save_options()
        print "gromacs updated"

    ##This function will create initial topology and trajectory using pdb file and choosen force field
    def pdb2top(self, file_path, project_name):
        status = ["ok", "Calculating topology using Force fields"]
        status_update(status)
        hh = "-"+self.hydro
        try:
            os.remove(project_name+".gro")
            os.remove(project_name+".top")
        except:
            pass

        fo = open("gromacs_stdin.txt", "w")
        fo.write( "%s\n" % str(self.force))
        fo.write( "%s" % str(self.water))
        fo.close()

        command = gromacs.command +" pdb2gmx -f " + project_name + ".pdb -o " + project_name + ".gro -p " + project_name + ".top " + hh
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+".gro") == True:
            status = ["ok", ""]
        else:
            status = ["fail", "Warning. Trying to ignore unnecessary hydrogen atoms."]
            status_update(status)

            command = gromacs.command+" pdb2gmx -ignh -f "+project_name+".pdb -o "+project_name+".gro -p "+project_name+".top "+hh
            executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+".gro") == True and stop == 0:
            status = ["ok", "Calculated topology using Force fields"]
        else:
            status = ["fail", "Force field unable to create topology file"]
        return status

    ##This is alternative function to create initial topology and triectory using pdb file
    def x2top(self, file_path, project_name):
        status = ["ok", "Calculating topology using Force fields"]
        status_update(status)
        try:
            os.remove(project_name+".gro")
            os.remove(project_name+".top")
        except:
            pass

        command = gromacs.command+" x2top -f "+project_name+".pdb -o "+project_name+".top"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+".top") == True and stop == 0:
            status = ["ok", "Calculating structure using trjconv."]
        else:
            status = ["fail", "Unable to create topology file."]
        status_update(status)

        if   status[0] == "ok":
            fo = open("gromacs_stdin.txt", "w")
            fo.write( "0")
            fo.close()

            command = gromacs.command+" trjconv -f "+project_name+".pdb -s "+project_name+".pdb -o "+project_name+".gro"
            executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

            if os.path.isfile(file_path+".gro") == True and stop == 0:
                status = ["ok", "Calculated structure using trjconv."]
            else:
                status = ["fail", "Unable to create structure file."]
        return status

    ##This function will create and add waterbox.
    def waterbox(self, file_path, project_name):
        status = ["ok", "Generating waterbox"]
        box_type = "-bt "+self.box_type+" "
        distance = "-d "+self.box_distance+" "
        density = "-density "+self.box_density

        try:
            os.remove(project_name+"1.gro")
            os.remove(project_name+"_solv.gro")
        except:
            pass

        status_update(status)
        command = gromacs.command+" editconf -f "+project_name+".gro -o "+project_name+"1.gro -c "+box_type+distance+density
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        water_name = gromacs.water_list[self.water-1][1][4:8].lower()
        print water_name
        if water_name == "tip4":
            water_gro = "tip4p.gro"
        elif water_name == "tip5":
            water_gro = "tip5p.gro"
        else:
            water_gro = "spc216.gro"

        command = gromacs.command+" solvate -cp "+project_name+"1.gro -cs "+water_gro+" -o "+project_name+"_solv.gro -p "+project_name+".top"

        status = ["ok", "Adding Water Box"]
        status_update(status)

        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"1.gro") == True and stop == 0:
            status = ["ok", "Water Box Added"]
        else:
            status = ["fail", "Unable to add water box"]
        return status

    ##This function will add ions/salts to the protein in waterbox
    def saltadd(self, file_path, project_name):
        status = ["ok", "Preparing to add ions or salt"]
        salt = "-conc "+self.salt_conc+" "
        positive = "-pname "+self.positive_ion+" "
        negative = "-nname "+self.negative_ion+" "
        neu ="-"+self.neutrality
        try:
            os.remove(project_name+"_b4em.gro")
            os.remove(project_name+"_ions.tpr")
        except:
            pass

        command = gromacs.command+" grompp -f em -c "+project_name+"_solv.gro -o "+project_name+"_ions.tpr -p "+project_name+".top"
        status_update(status)
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        fo = open("gromacs_stdin.txt", "w")
        fo.write( "13")
        fo.close()

        status = ["ok", "Adding salts and ions"]
        status_update(status)

        command = gromacs.command+" genion -s "+project_name+"_ions.tpr -o "+project_name+"_b4em.gro "+positive+negative+salt+neu+" -p "+project_name+".top"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_b4em.gro") == True and stop == 0:
            status = ["ok", "Ions added successfully"]
        elif stop == 0:
            status = ["ok", "Find out what's wrong!"]
        else:
            status = ["failed", "Unable to add ions"]
        return status

    ##This function will perform energy minimization    
    def em(self, file_path, project_name):
        status = ["ok", "Energy Minimization"]

        try:
            os.remove(project_name+"_em.tpr")
            os.remove(project_name+"_em.trr")
            os.remove(project_name+"_b4pr.gro")
        except:
            pass

        ##Check if waterbox was added and adjust accordingly.
        if not os.path.isfile(file_path+"_b4em.gro"):
            shutil.copy(project_name+".gro", project_name+"_b4em.gro")

        status_update(status)       
        command = gromacs.command+" grompp -f em -c "+project_name+"_b4em -p "+project_name+" -o "+project_name+"_em"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        command = gromacs.command+" mdrun -nice 4 -s "+project_name+"_em -o "+project_name+"_em -c "+project_name+"_b4pr -v"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_em.tpr") == True and stop == 0:
            status = ["ok", "Energy Minimized"]
        else:
            status = ["fail", "Unable to perform Energy Minimization"]
        return status

    ##This function will perform position restrained MD
    def pr(self, file_path, project_name):
        status = ["ok", "Position Restrained MD"]

        try:
            os.remove(project_name+"_pr.tpr")
            os.remove(project_name+"_pr.trr")
            os.remove(project_name+"_b4md.gro")
        except:
            pass

        status_update(status)
        command = gromacs.command+" grompp -f pr -c "+project_name+"_b4pr -r "+project_name+"_b4pr -p "+project_name+" -o "+project_name+"_pr"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        command = gromacs.command+" mdrun -nice 4 -s "+project_name+"_pr -o "+project_name+"_pr -c "+project_name+"_b4md -v"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_pr.tpr") == True and stop == 0:
            status = ["ok", "Position Restrained MD finished"]
        else:
            status = ["fail", "Unable to perform Position Restrained"]
        return status

    ##This function will create posre.itp file for molecular dynamics simulation with choosen atoms if restraints were selected
    def restraints(self, project_name):
        status = ["ok", "Adding Restraints"]

        try:
            os.remove("posre_2.itp")
        except:
            pass

        fo = open("gromacs_stdin.txt", "w")
        fo.write( "0")
        fo.close()

        status_update(status)
        command = gromacs.command+" genrestr -f "+project_name+".pdb -o posre_2.itp -n index_dynamics.ndx"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile("posre_2.itp") == True and stop == 0:
            status = ["ok", "Added Restraints"]
            if os.path.isfile("posre.itp"):
                os.remove("posre.itp")
            shutil.copy("posre_2.itp", "posre.itp")
        else:
            status = ["fail", "Unable to create restraints file"]
        return status

    ##This function will perform position final molecular dynamics simulation
    def md(self, file_path, project_name):
        status = ["ok", "Molecular Dynamics Simulation"]

        try:
            os.remove(project_name+"_md.tpr")
            os.remove(project_name+"_md.trr")
        except:
            pass

        ##Check if em and/or pr was done and adjust accordingly.
        if not os.path.isfile(file_path+"_b4md.gro"):
            if not os.path.isfile(file_path+"_b4pr.gro"):
                #No em and pr
                shutil.copy(project_name+"_b4em.gro", project_name+"_b4md.gro")
            else:
                #No pr
                shutil.copy(project_name+"_b4pr.gro", project_name+"_b4md.gro")

        status_update(status)
        command = gromacs.command+" grompp -f md -c "+project_name+"_b4md  -p "+project_name+" -o "+project_name+"_md"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        command = gromacs.command+" mdrun -nice 4 -s "+project_name+"_md -o "+project_name+"_md -c "+project_name+"_after_md -v"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_md.tpr") == True and stop == 0:
            status = ["ok", "Molecular Dynamics Simulation finished"]
        else:
            status = ["fail", "Unable to perform Molecular Dynamics Simulation"]
        return status

    ##This function will convert final results to multimodel pdb file
    def trjconv(self, file_path, project_name):
        status = ["ok", "Creating Multimodel PDB"]

        try:
            os.remove(project_name+"_multimodel.pdb")
        except:
            pass
        if os.path.isfile(project_name+"_multimodel.pdb") == True:
            os.remove(project_name+"_multimodel.pdb")

        fo = open("gromacs_stdin.txt", "w")
        fo.write( "%s" % str(self.group))
        fo.close()

        status_update(status)
        command = gromacs.command+" trjconv -f "+project_name+"_md.trr -s "+project_name+"_md.tpr -o "+project_name+"_multimodel.pdb"
        executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_multimodel.pdb") == True and stop == 0:
            status = ["ok", "Finished!"]
        else:
            status = ["fail", "Unable to generate multimodel PDB file"]
        return status

##This class will handle PCA by ProDy python library and show vectors from NMD file.
class Vectors:

    nmd_name = []
    nmd_atomnames = []
    nmd_resnames = []
    nmd_resids = []
    nmd_bfactors = []
    nmd_coordinates = []
    nmd_mode = []
    color="gray"
    scale = 1.0
    mode_nr = 0

    calculation_type = 0
    contact_map = 0
    block_contact_map = 0

    enm = 0

    ##Change Multimodel PDB file into NMD vector file
    def prody(self):
        #Silence ProDy and create logs
        prody.confProDy(verbosity='none')
        prody.startLogfile("log_prody.log")
        #Prepare ensemble
        model = prody.parsePDB(project_name+"_multimodel.pdb", subset='calpha')
        model
        ensemble = prody.Ensemble(project_name+' ensemble')
        ensemble.setCoords(model.getCoords())
        ensemble.addCoordset(model.getCoordsets())
        ensemble.iterpose()
        #ANM calculations
        if self.calculation_type == 0:
            anm = prody.ANM(project_name)
            anm.buildHessian(ensemble)
            anm.calcModes()
            anm
            write_nmd = anm
            self.enm = anm
        #PCA calculations
        elif self.calculation_type == 1:
            pca = prody.PCA(project_name)
            pca.buildCovariance(ensemble)
            pca.calcModes()
            write_nmd = pca
        #GNM calculations
        elif self.calculation_type == 2:
            gnm = prody.GNM(project_name)
            gnm.buildKirchhoff(ensemble)
            gnm.calcModes()
            gnm
            write_nmd = gnm
            self.enm = gnm
        #Write NMD file
        prody.writeNMD(project_name+'.nmd', write_nmd[:3], model)
        prody.closeLogfile("log_prody.log")

    ##Read NMD file 
    def nmd_format(self):
        file_nmd = open(project_name+'.nmd',"r")
        list_nmd = file_nmd.readlines()

        self.nmd_mode=[]
        self.nmd_scale_mode=[]
        for line in list_nmd:
            split_line = line.split()
            if split_line[0] == "name":
                self.nmd_name = split_line
                self.nmd_name.pop(0)
            elif split_line[0] == "atomnames":
                self.nmd_atomnames = split_line
                self.nmd_atomnames.pop(0)
            elif split_line[0] == "resnames":
                self.nmd_resnames = split_line
                self.nmd_resnames.pop(0)
            elif split_line[0] == "resids":
                self.nmd_resids = split_line
                self.nmd_resids.pop(0)
            elif split_line[0] == "bfactors":
                self.nmd_bfactors = split_line
                self.nmd_bfactors.pop(0)
            elif split_line[0] == "coordinates":
                self.nmd_coordinates = split_line
                self.nmd_coordinates.pop(0)
            elif split_line[0] == "mode":
                pre_mode = split_line
                self.nmd_mode.append(pre_mode[3:])
                self.nmd_scale_mode.append(pre_mode[2])

    ##Show contact map on PyMOL screen
    def show_contact_map(self, sensitivity):
        contact_matrix = self.enm.getKirchhoff()
        print contact_matrix
        c_alpha_nr = 0
        for c_alpha_list in contact_matrix:
            c_alpha_nr = c_alpha_nr + 1
            c_alpha_target_nr = 0
            for c_alpha_1 in c_alpha_list:
                c_alpha_target_nr = c_alpha_target_nr + 1
                if c_alpha_nr != c_alpha_target_nr and float(c_alpha_1) < float(sensitivity):
                    cmd.select("sele1", "n. ca and "+project_name+"_multimodel and i. "+str(c_alpha_nr)) #PyMOL API
                    cmd.select("sele2", "n. ca and "+project_name+"_multimodel and i. "+str(c_alpha_target_nr)) #PyMOL API
                    cmd.distance("contact_map", "sele1", "sele2") #PyMOL API
        try:
            cmd.hide("labels", "contact_map") #PyMOL API
            cmd.delete("sele1") #PyMOL API
            cmd.delete("sele2") #PyMOL API
        except:
            pass

    ##Show contact map/cross corelation as a graph
    def graph_contact_map(self, plot_type):
        if plot_type == "contact":
            #matplotlib
            prody.showContactMap(self.enm)
        elif plot_type == "cross":
            #matplotlib
            prody.showCrossCorr(self.enm)

    ##Show vectors from NMD file
    def show_vectors(self):
        color1 = list(cmd.get_color_tuple(self.color)) #PyMOL API
        color2 = list(cmd.get_color_tuple(self.color)) #PyMOL API
        arrow_head_radius= 0.15

        x1=[]
        y1=[]
        z1=[]

        coor = "x"
        for coordinate in self.nmd_coordinates:
            if coor == "x":
                x1.append(float(coordinate))
                coor = "y"
            elif coor == "y":
                y1.append(float(coordinate))
                coor = "z"
            elif coor == "z":
                z1.append(float(coordinate))
                coor = "x"

        x2=[]
        y2=[]
        z2=[]

        #This factor is provided to make vector length more like in NMWiz. More investigation is needed to get exact formula.
        approximation_factor = 16.6

        coor = "x"
        coor_nr = 0
        round_nr = 0
        for mode in self.nmd_mode[self.mode_nr]:
            if coor == "x":
                x2.append(float(mode) * float(self.nmd_scale_mode[self.mode_nr]) * approximation_factor * self.scale + x1[coor_nr])
                coor = "y"
            elif coor == "y":
                y2.append(float(mode) * float(self.nmd_scale_mode[self.mode_nr]) * approximation_factor * self.scale + y1[coor_nr])
                coor = "z"
            elif coor == "z":
                z2.append(float(mode) * float(self.nmd_scale_mode[self.mode_nr]) * approximation_factor * self.scale + z1[coor_nr])
                coor = "x"
            round_nr = round_nr + 1
            if round_nr == 3:
                round_nr = 0
                coor_nr = coor_nr + 1

        coor_nr = 0
        cam_possition = cmd.get_view(quiet=1) #PyMOL API
        for position in x1:
            try:
                cmd.delete("Mode_Vector_"+ str(coor_nr))
            except:
                pass

            cone=[cgo.CONE, x1[coor_nr], y1[coor_nr], z1[coor_nr], x2[coor_nr], y2[coor_nr], z2[coor_nr], arrow_head_radius, 0.0] + color1 + color2 + [1.0, 0.0 ]
            cmd.load_cgo(cone,"Mode_Vector_"+ str(coor_nr)) # PyMOL API
            coor_nr = coor_nr+1
        cmd.set_view(cam_possition) #PyMOL API

    def change_vectors_color(self, color):
        self.color = color
        self.show_vectors()

    def change_vectors_scale(self, scale):
        scale = float(scale)
        self.scale = scale
        self.show_vectors()

    def change_vectors_mode_nr(self, mode_nr):
        self.mode_nr = mode_nr
        self.show_vectors()

    #This is the window to setup ProDy options
    def window(self, master):
        if project_name != "nothing":
            root = Toplevel(master)
            root.wm_title("Vectors Configuration")

            frame1 = Frame(root)
            frame1.pack()

            v1 = IntVar(root)
            v1.set(self.calculation_type)
            v2 = IntVar(root)
            v2.set(self.contact_map)

            radio_button0 = Radiobutton(frame1, text="Anisotropic network model", value=0, variable=v1, command = lambda : self.block_contact(0, c1, v2))
            radio_button0.pack()
            radio_button1 = Radiobutton(frame1, text="Principal component analysis", value=1, variable=v1, command = lambda : self.block_contact(1, c1, v2))
            radio_button1.pack()
            radio_button2 = Radiobutton(frame1, text="Gaussian network model (experimental)", value=2, variable=v1, command = lambda : self.block_contact(0, c1, v2))
            radio_button2.pack()

            c1 = Checkbutton(frame1, text="Show Contact Map", variable=v2)
            c1.pack()
            if self.block_contact_map == 1:
                c1.configure(state=DISABLED)

            ok_button = Button(frame1, text = "OK", command=lambda : self.options_change(v1, v2, root))
            ok_button.pack(side=TOP)

        elif project_name == "nothing":
            no_molecule_warning()

    def options_change(self, v1, v2, root):
        self.calculation_type = v1.get()
        self.contact_map = v2.get()
        save_options()
        root.destroy()

    def block_contact(self, block, contact_map_b, contact_map_v):
        self.block_contact_map = block
        if block == 0:
            contact_map_b.configure(state=ACTIVE)
        elif block == 1:
            contact_map_b.configure(state=DISABLED)
            contact_map_v.set(0)

##This class create and maintain abstraction mdp file representatives. em.mdp, pr.mdp, md.mdp
class Mdp_config:

    external_file=0
    options = [[]]
    file_name = ""

    def __init__(self, file_name, init_config, external_file=0):
        self.file_name = file_name
        self.external_file = external_file
        list1 = init_config.split("\n")
        list2 = []
        for line in list1:
            list2.append(line.split(" = "))
        self.options = list2            

    def update(self, option_nr, value, check=1):
        self.options[option_nr][1] = value
        if check == 0 and self.options[option_nr][0][0] != ";":
            self.options[option_nr][0] = ";"+self.options[option_nr][0]
        elif check == 1 and self.options[option_nr][0][0] == ";":
            self.options[option_nr][0] = self.options[option_nr][0][1:]
        self.clean_artefacts()

    def save_file(self):
        config = ""
        for option in self.options:
            #pass empty option
            if option == ['']:
                pass
            else:
                config = config + option[0]+" = "+option[1]+"\n"
        mdp = open(project_dir+self.file_name, "w")
        mdp.write(config)
        mdp.close() 

    #Clean options from artefacts
    def clean_artefacts(self):  
        try:
            self.options.remove([''])
        except:
            pass

##Status and to_do maintaining class
class Progress_status:

    #0:Save configuration files; 1:Generate topology file from pdb; 2:Adding Water Box; 3: Adding ions and neutralization 4:Energy Minimization; 5:Position Restrained MD; 6:Restraints; 7:Molecular Dynamics Simulation; 8:Generate multimodel PDB; 9:Calculate vectors using ProDy
    status= [0,0,0,0,0,0,0,0,0,0]
    to_do = [1,1,1,1,1,1,0,1,1,1]

    resume = 0
    x2top = 0
    steps = 8

    def to_do_update(self, position, value):
        if type(position) == type(1):
            self.to_do[position] = value
            self.to_do = self.to_do
            save_options()

    def x2top_update(self, value):
        if type(value) == type(1):
            self.x2top = value

    def to_do_status(self):
        to_do = []
        for work in self.status:
            if work == 0:
                to_do.append(1)
            elif work == 1:
                to_do.append(0)
        self.to_do = to_do

##init function - puts plugin into menu and starts 'init_function' after clicking.
def __init__(self):
    self.menuBar.addmenuitem("Plugin", "command", "Dynamics_Gromacs"+plugin_ver, label = "Dynamics_Gromacs"+plugin_ver,
    command = init_function)

# Detect gmx executable along with other associated information...
def getGromacsExeInfo():
    gmxExes = ['gmx_mpi_d', 'gmx_mpi', 'gmx']

    gmxExe = ""
    version = ""
    buildArch = ""
    buildOnCygwin = 0

    stdoutFile = "test_gromacs.txt"
    if os.path.isfile(stdoutFile):
        os.remove(stdoutFile)

    for gmx in gmxExes:
        cmd = gmx + " -version"
        executeSubprocess(cmd,  None, stdoutFile)

        ofs = open(stdoutFile, "r")
        output = ofs.read()
        ofs.close()

        output = standardizeNewLineChar(output)
        if not re.search("GROMACS version:", output, re.I):
            continue

        gmxExe = gmx
        for line in output.split("\n"):
            if re.search("^[ ]*GROMACS version:", line, re.I):
                gmxExe = gmx
                version = re.sub("^[ ]*GROMACS version:[ ]*", "", line, flags = re.I)
                if "VERSION " in version:
                    version = version.split("VERSION ")[1].rstrip()
            elif re.search(r"^[ ]*Build OS/arch:", line, re.I):
                buildArch = re.sub("^[ ]*Build OS/arch:[ ]*", "", line, flags = re.I)

                if re.search(r"CYGWIN", buildArch, re.I):
                    buildOnCygwin = 1
        break

    return (gmxExe, version, buildArch, buildOnCygwin)

# Setup directories for running gmx...
def setGromacsDynamicsAndProjectDirs():
    global project_name, dynamics_dir, project_dir

    project_name = "nothing"

    homeDir = expanduser("~")

    gmxHomeDirPath = os.path.abspath(homeDir)
    dynamics_dir = os.path.join(gmxHomeDirPath, '.dynamics', '')
    project_dir = os.path.join(dynamics_dir, project_name, '')

# Setup project directory for running gmx...
def setGromacsProjectDir():
    global project_name, project_dir
    project_dir = os.path.join(dynamics_dir, project_name, '')

# Execute command using stdin/stdout as needed...
def executeSubprocess(command, stdinFilePath = None, stdoutFilePath = None):
    stdinFile = None
    stdinMsg = "None"
    if stdinFilePath:
        stdinFile = open(stdinFilePath, "r")
        stdinMsg = stdinFilePath

    stdoutFile = None
    stdoutMsg = "None"
    if stdoutFilePath:
        stdoutFile = open(stdoutFilePath, "w")
        stdoutMsg = stdoutFilePath

    print "Running command: " + command + "; STDIN: " + stdinMsg + "; STDOUT: " + stdoutMsg

    returnCode = subprocess.call("bash -lic '" + command + " '", stdin=stdinFile, stdout=stdoutFile, stderr=subprocess.STDOUT, shell=True)

    if stdinFilePath:
        stdinFile.close()
    if stdoutFilePath:
        stdoutFile.close()

    return returnCode

# Strat a subprocess and wait for it to complete along with an option to kill it...
def executeAndMonitorSubprocess(command, stdinFilePath = None, stdoutFilePath = None, logFilePath = None):
    global stop

    if logFilePath:
        if os.path.isfile(logFilePath):
            logFile = open(logFilePath, 'a')
        else:
            logFile = open(logFilePath, 'w')
        logFile.write("\n!************************!\n" + command + "\n!************************!\n")
        logFile.close()

    stdinFile = None
    stdinMsg = "None"
    if stdinFilePath:
        stdinFile = open(stdinFilePath, "r")
        stdinMsg = stdinFilePath

    stdoutFile = None
    stdoutMsg = "None"
    if stdoutFilePath:
        stdoutFile = open(stdoutFilePath, "w")
        stdoutMsg = stdoutFilePath

    print "Running command: " + command + "; STDIN: " + stdinMsg + "; STDOUT: " + stdoutMsg

    gmx = subprocess.Popen("bash -lic '" + command + " '",  stdin=stdinFile, stdout=stdoutFile, stderr=subprocess.STDOUT, shell=True)
    while gmx.poll() is None:
        if stop == 1:
            gmx.kill()
            break
        time.sleep(1.0)

    if stdinFilePath:
        stdinFile.close()

    if stdoutFilePath:
        stdoutFile.close()

    # Append any stdout to log file...
    if logFilePath and stdoutFilePath:
        logFile = open(logFilePath, "a")
        stdoutFile = open(stdoutFilePath, "r")
        logFile.write(stdoutFile.read())
        logFile.close()
        stdoutFile.close()

# Change Windows and Mac new line char to UNIX...
def standardizeNewLineChar(inText):
    outText = re.sub("(\r\n)|(\r)", "\n", inText)
    return outText

# Read text lines and standardize new line char...
def readTextLines(textFilePath):
    textLines = []

    ifs = open(textFilePath, "r")
    for line in iter(ifs.readline, ''):
        newLine = standardizeNewLineChar(line)
        textLines.append(newLine)
    ifs.close()

    return textLines

# Collect water modes information...
def getWaterModelsInfo(gmxOutputLines):
    startLine = 0
    while gmxOutputLines[startLine][0:7] != "Opening":
        startLine = startLine + 1

    startLine = startLine + 1
    endLine = startLine

    while (gmxOutputLines[endLine][0:7] != "Opening") and (gmxOutputLines[endLine][0] != "\n"):
        endLine = endLine + 1

    watersInfo = gmxOutputLines[startLine:endLine]
    watersInfo2 = []
    number = 1
    for water in watersInfo:
        watersInfo2.append([number, water[:-1]])
        number = number + 1

    return watersInfo2

##This function will initialize all plugin stufs
def init_function():
    ##Global variables
    global stop, status, error, em_init_config, pr_init_config, md_init_config, project_name, dynamics_dir, project_dir
    global gmxExe, gmxVersion, gmxBuildArch, gmxOnCygwin

    stop = 1
    status = ["ok", ""]
    error = ""

    # Make sure HOME environment variable is defined before setting up directories...
    homeDir = expanduser("~")
    if homeDir:
        os.chdir(homeDir)
    else:
        print "HOME environment variable not defined"
        status = ["fail", "HOME environment variable not defined. Please set its value and try again."]
        tkMessageBox.showerror("Initialization error", status[1])
        return
    setGromacsDynamicsAndProjectDirs()

    ## Clean up any temporary project directory...
    if os.path.isdir(project_dir):
        shutil.rmtree(project_dir)
    ## Create temporary project directory along with any subdirectories...
    if not os.path.isdir(project_dir):
        os.makedirs(project_dir)

    print "Searching for GROMACS installation"
    os.chdir(dynamics_dir)
    gmxExe, gmxVersion, gmxBuildArch, gmxOnCygwin = getGromacsExeInfo()
    os.chdir(homeDir)

    if not len(gmxExe):
        print "GROMACS 5 or newer not detected."
        status = ["fail", "GROMACS not detected. Please install and setup GROMACS 5 or newer correctly for your platform. Check '~/.dynamics/test_gromacs.txt' for more details. Don't forget to add GROMACS bin directory to your PATH"]
        tkMessageBox.showerror("Initialization error", status[1])
        return
    else:
        print "Found GROMACS VERSION " + gmxVersion

    ##Gromacs variables
    global gromacs, gromacs2

    gromacs = Gromacs_output()
    gromacs2 = Gromacs_input()

    em_init_config = """define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 10000
nstlist = 10
ns_type = simple
rlist = 1.5
rcoulomb = 1.5
rvdw = 1.5
emtol = 1000.0
emstep = 0.01
implicit-solvent = no
;gb-algorithm = Still
;pbc = no
;rgbradii = 0
cutoff-scheme = Verlet
coulombtype = PME"""
    pr_init_config = """define = -DPOSRES
constraints = all-bonds
integrator = md-vv
dt = 0.002
nsteps = 5000
nstcomm = 1
nstxout = 100
nstvout = 100
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = simple
rlist = 1.5
rcoulomb = 1.5
rvdw = 1.5
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein Non-Protein
ref_t = 298 298
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 298.0
gen_seed = 173529
cutoff-scheme = Verlet
coulombtype = PME"""
    md_init_config = """;define = -DPOSRES
integrator = md-vv
dt = 0.002
nsteps = 5000
nstcomm = 1
nstxout = 50
nstvout = 50
nstfout = 0
nstlist = 10
ns_type = simple
rlist = 1.5
rcoulomb = 1.5
rvdw = 1.5
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein Non-Protein
ref_t = 298 298
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 298.0
gen_seed = 173529
constraints = all-bonds
constraint-algorithm = Lincs
continuation = no
shake-tol = 0.0001
lincs-order = 4
lincs-warnangle = 30
morse = no
implicit-solvent = no
;gb-algorithm = Still
;pbc = no
;rgbradii = 0
;comm_mode = ANGULAR
cutoff-scheme = Verlet
coulombtype = PME"""        

    ##Prody variables
    if prody_true == 1:
        global vectors_prody
        vectors_prody = Vectors()
        print "ProDy correctly imported"

    ##Creating objects - data from those windows will be used by rootWindow
    if status[0] == "ok":
        global calculationW, waterW, restraintsW, genionW
        calculationW = CalculationWindow()
        waterW = WaterWindows()
        restraintsW = RestraintsWindow()
        genionW = GenionWindow()
        ##Start graphic interface
        rootWindow()
    ##Break now if status is not ok and print message
    elif status[0] == "fail":
        tkMessageBox.showerror("Initialization error", status[1])

##--Graphic Interface--
##Root menu window
def rootWindow():

    root = Tk()
    balloon = Pmw.Balloon(root)
    root.wm_title("Dynamics with Gromacs"+plugin_ver)

    ##Detect list of PyMOL loaded PDB files if no files than list "nothing"
    allNames = cmd.get_names("objects") #PyMOL API
    allNames1 = []
    for name in allNames:
        name1 = name.split("_")
        if name1[-1] == "multimodel" or name1[-1] == "(sele)" or (name1[0] == "Mode" and len(name1) == 3):
            pass
        else:
            allNames1.append(name)
    allNames = allNames1

    if allNames == []:
        allNames = ["nothing"]

    ##TkInter variables
    global project_dir, project_name, molecule_from_pymol
    project_name = allNames[0]
    setGromacsProjectDir()
    if allNames != ["nothing"]:
        create_config_files()

    v1_name = StringVar(root)
    v1_name.set(project_name)

    groupNr = gromacs.group_list[1][0]
    v2_group = IntVar(root)
    v2_group.set(groupNr)

    forceNr = gromacs.force_list[0][0]
    v3_force = IntVar(root)
    v3_force.set(forceNr)

    waterNr = gromacs.water_list[0][0]
    v4_water = IntVar(root)
    v4_water.set(waterNr)

    water_v = StringVar(root)
    water_v.set(gromacs.water_list[0][1])

    time_entry_value = StringVar(root)
    time_entry_value.set("10.0")

    ##Start drawing interface
    frame0 = Frame(root)
    frame0.pack(side=TOP)

    w_version = Label(frame0, text="GROMACS VERSION " + gromacs.version)
    w_version.pack(side=TOP)

    frame1 = Frame(root)
    frame1.pack(side=TOP)

    frame1_1 = Frame(frame1, borderwidth=1, relief=RAISED)
    frame1_1.pack(side=LEFT)

    w1 = Label(frame1_1, text="Molecules", font = "bold")
    w1.pack(side=TOP)

    frame1_1a = Frame(frame1_1)
    frame1_1a.pack(side=TOP)

    #List of PyMOL loaded PDB files
    if allNames[0] != "nothing":
        for molecule in allNames:
            radio_button1 = Radiobutton(frame1_1a, text=molecule, value=molecule, variable=v1_name, command=lambda: set_variables(v1_name.get(), v2_group, v3_force, v4_water, water_v, check1_button))
            radio_button1.pack(side=TOP, anchor=W)
            #Tooltip
            balloon.bind(radio_button1, "Select molecule for calculations")
    #If no loaded PDB files, than add button to choose one
    else:
        w1_1 = Label(frame1_1a, text="Choose PDB file")
        w1_1.pack(side=TOP)
        frame1_1_1 = Frame(frame1_1a)
        frame1_1_1.pack(side=TOP)
        label1 = Label(frame1_1_1, textvariable=v1_name)
        label1.pack(side=LEFT)
        button_e1 = Button(frame1_1_1, text = "Browse", command=lambda: select_file(v1_name))
        button_e1.pack(side=LEFT)
        #Tooltip
        balloon.bind(button_e1, "Select molecule for calculations")

    #List of previous projects
    if os.path.isdir(dynamics_dir) == True:
        projects = os.listdir(dynamics_dir)
    else:
        projects = []
    projects2 = []
    for file_dir in projects:
        if os.path.isdir(dynamics_dir + file_dir) and file_dir not in allNames and file_dir != "nothing":
            projects2.append(file_dir)
    if projects2 != []:
        w1_2 = Label(frame1_1, text="Previous Projects")
        w1_2.pack(side=TOP)

        for molecule in projects2:
            molecule1 = molecule.split("_")
            if molecule1[-1] == "multimodel":
                pass
            else:
                molecule1 = molecule.split("-")
                if molecule1[0] == "gromacs":
                    pass
                else:
                    radio_button1 = Radiobutton(frame1_1, text=molecule, value=molecule, variable=v1_name, command=lambda: set_variables(v1_name.get(), v2_group, v3_force, v4_water, water_v, check1_button))
                    radio_button1.pack(side=TOP, anchor=W)
                    #Tooltip
                    balloon.bind(radio_button1, "Select molecule for calculations")

    #List of group for final model
    w2 = Label(frame1_1, text="Group", font = "bold")
    w2.pack(side=TOP)
    for group in gromacs.group_list:
        radio_button2 = Radiobutton(frame1_1, text=group[1], value=group[0], variable=v2_group, command=lambda: gromacs2.update({"group" : v2_group.get()}))
        radio_button2.pack(side=TOP, anchor=W)
        #Tooltip
        balloon.bind(radio_button2, "Select group of atoms for final display")

    frame1_2 = Frame(frame1, borderwidth=1, relief=RAISED)
    frame1_2.pack(side=LEFT)

    #List of available force fields
    w3 = Label(frame1_2, text="Force fields", anchor=E, font = "bold")
    w3.pack(side=TOP)

    for force in gromacs.force_list:
        radio_button3 = Radiobutton(frame1_2, text=force[1], value=force[0], variable=v3_force, command=lambda : waterW.change(v4_water, water_v, v3_force.get()))
        radio_button3.pack(side=TOP, anchor=W)
        #Tooltip
        balloon.bind(radio_button3, "Select force field which will be used for dynamics simulation")

    #Label of choosen water model
    w4 = Label(frame1_2, text="Water Model", anchor=E, font = "bold")
    w4.pack(side=TOP)

    frame1_2_1 = Frame(frame1_2)
    frame1_2_1.pack(side=TOP)

    #Buttons to choose water model and configure water box
    water_label = Label(frame1_2_1, textvariable=water_v)
    water_label.pack(side=LEFT)
    water_button = Button(frame1_2_1, text = "Choose...", command=lambda : waterW.choose(v4_water, water_v, waterbox_button, root))
    water_button.pack(side=LEFT)
    waterbox_button = Button(frame1_2_1, text = "Configure", command=lambda: waterW.box(root))
    waterbox_button.pack(side=LEFT)
    waterbox_button2 = Button(frame1_2_1, text = "Hydrogen Mass", command=lambda: waterW.box2(root))
    waterbox_button2.pack(side=LEFT)

    frame1_3 = Frame(frame1)
    frame1_3.pack(side=LEFT)

    frame1_3_1 = Frame(frame1_3, borderwidth=1, relief=RAISED)
    frame1_3_1.pack(side=TOP)

    w4 = Label(frame1_3_1, text="Configuration", font = "bold")
    w4.pack(side=TOP)

    #Button for configuration of Simulation Steps
    steps_label = Label(frame1_3_1, text="Simulation Steps")
    steps_label.pack(side=TOP)
    steps_button = Button(frame1_3_1, text = "Configure", command=lambda: steps_configure(root, check1_button))
    steps_button.pack(side=TOP)

    #Button for Genion configuration
    ion_label = Label(frame1_3_1, text="Adding ions & Neutralize")
    ion_label.pack(side=TOP)
    ion_button2 = Button(frame1_3_1, text = "Configure", command=lambda: genionW.window(root))
    ion_button2.pack(side=TOP)

    #Button for configuration of MDP files
    em_label = Label(frame1_3_1, text="Energy Minimization")
    em_label.pack(side=TOP)
    em_button2 = Button(frame1_3_1, text = "Configure", command=lambda: mdp_configure("em", root))
    em_button2.pack(side=TOP)
    if os.path.isfile(dynamics_dir + "em.mdp"):
        em_button2.configure(state=DISABLED)

    pr_label = Label(frame1_3_1, text="Position Restrained MD")
    pr_label.pack(side=TOP)
    pr_button2 = Button(frame1_3_1, text = "Configure", command=lambda: mdp_configure("pr", root))
    pr_button2.pack(side=TOP)
    if os.path.isfile(dynamics_dir + "pr.mdp"):
        pr_button2.configure(state=DISABLED)

    md_label = Label(frame1_3_1, text="Molecular Dynamics Simulation")
    md_label.pack(side=TOP)
    md_button2 = Button(frame1_3_1, text = "Configure", command=lambda: mdp_configure("md", root))
    md_button2.pack(side=TOP)
    if os.path.isfile(dynamics_dir + "md.mdp"):
        md_button2.configure(state=DISABLED)

    #Button for configuration of Restraints
    re_label = Label(frame1_3_1, text="Restraints (Select Atoms)")
    re_label.pack(side=TOP)

    check1_button = Button(frame1_3_1, text = "Configure", command=lambda: restraintsW.window(root))
    check1_button.pack(side=TOP)

    #Button for ProDy options
    pro_label = Label(frame1_3_1, text="Vectors Options")
    pro_label.pack(side=TOP)
    prody_button = Button(frame1_3_1, text = "Configure", command=lambda: vectors_prody.window(root))
    prody_button.pack(side=TOP)

    #Dynamics Simulation Time
    time_label = Label(frame1_3_1, text="Dynamics Simulation Time")
    time_label.pack(side=TOP)

    frame1_3_1_1 = Frame(frame1_3_1)
    frame1_3_1_1.pack(side=TOP)

    time_entry = Entry(frame1_3_1_1, textvariable=time_entry_value)
    time_entry.pack(side=LEFT)
    time_label2 = Label(frame1_3_1_1, text="[ps]")
    time_label2.pack(side=LEFT)
    time_button = Button(frame1_3_1_1, text = "OK", command=lambda: md_file.update(3, int(float(time_entry_value.get())/float(md_file.options[2][1]))))
    time_button.pack(side=LEFT)

    ##Disable configuration of ProDy (Vectors) if ProDy is not installed
    if prody_true != 1:
        prody_button.configure(state=DISABLED)

    frame2 = Frame(root)
    frame2.pack(side=TOP)

    #Additional Buttons
    exit_button = Button(frame2, text = "Exit", command=root.destroy)
    exit_button.pack(side=LEFT)

    clean_button = Button(frame2, text = "Clean", command=cleanMessage)
    clean_button.pack(side=LEFT)

    help_button = Button(frame2, text = "Help", command=lambda: helpWindow(root))
    help_button.pack(side=LEFT)

    save_button = Button(frame2, text = "Save", command=select_file_save)
    save_button.pack(side=LEFT)

    load_button = Button(frame2, text = "Load", command=lambda: select_file_load(frame1_1a, v1_name, v2_group, v3_force, v4_water, water_v, check1_button))
    load_button.pack(side=LEFT)

    count_button = Button(frame2, text = "OK", command=lambda: calculationW.check_window(root))
    count_button.pack(side=LEFT)

    #Initial configuration
    set_variables(v1_name.get(), v2_group, v3_force, v4_water, water_v, check1_button)

    #Tooltips
    balloon.bind(water_button, "Choose one of the Water Models for dynamics simulation")
    balloon.bind(waterbox_button, "Configure Water Model parameters")
    balloon.bind(waterbox_button2, "Use Deuterium or Heavier hydrogens (to allow bigger time steps in MD)")
    balloon.bind(steps_button, "Select calculations which needs to be performed for dynamics simulation")
    balloon.bind(ion_button2, "Select salt concentration and neutralization status")
    balloon.bind(em_button2, "Configure Energy Minimization parameters")
    balloon.bind(pr_button2, "Configure Position Restrained MD parameters")
    balloon.bind(md_button2, "Configure Molecular Dynamics Simulation parameters")
    balloon.bind(check1_button, "Selecet which atoms should be restrainted (unlock in Simulation Steps)")
    balloon.bind(exit_button, "Exit the Plugin")
    balloon.bind(clean_button, "Remove all temporary files (including previous projects)")
    balloon.bind(help_button, "Display short help")
    balloon.bind(save_button, "Save current project to tar.bz2 archive")
    balloon.bind(load_button, "Load tar.bz2 archive with project files for further processing")
    balloon.bind(count_button, "Go to the next window and perform Molecular Dynamics Simulation")
    if prody_true == 1:
        balloon.bind(prody_button, "Set vectors options")
    else:
        balloon.bind(prody_button, "In order to use this option install ProDy")

    root.mainloop()

##Molecular Dynamics Performing window
class CalculationWindow:

    tasks_to_do = 0
    bar_var = ""
    bar_widget = ""
    start_button = ""
    stop_button = ""
    log_button = ""

    def __init__(self):
        self.queue_status = Queue.Queue()
        self.queue_percent = Queue.Queue()

    ##This will prevent Calculation Window to display if non protein has been selected
    def check_window(self, master):
        if project_name != "nothing":
            master.destroy()
            root = Tk()
            self.window(root)
            root.mainloop()
        elif project_name == "nothing":
            no_molecule_warning()

    ##This function will create main Calculation Window
    def window(self, root):
        print project_name
        balloon = Pmw.Balloon(root)
        root.wm_title("Calculation Window")
        frame1 = Frame(root)
        frame1.pack(side=TOP)
        frame2 = Frame(root)
        frame2.pack(side=TOP)

        self.bar_var = StringVar(root)
        self.bar_var.set("Ready to start")

        w5 = Label(frame1, textvariable=self.bar_var)
        w5.pack(side=TOP)
        self.bar_widget = Progressbar(frame1)
        self.bar_widget.pack(side=TOP)

        exit_button = Button(frame2, text = "EXIT", command=root.destroy)
        exit_button.pack(side=LEFT)

        save_button = Button(frame2, text = "SAVE", command=lambda: select_file_save(1))
        save_button.pack(side=LEFT)

        stop_button = Button(frame2, text = "STOP", command=lambda : self.start_counting(0))
        stop_button.pack(side=LEFT)
        if stop == 1:
            stop_button.configure(state=DISABLED)
        self.stop_button = stop_button

        start_button = Button(frame2, text = "START", command=lambda: self.start_counting(1))
        start_button.pack(side=LEFT)
        if stop == 0:
            start_button.configure(state=DISABLED)
        self.start_button = start_button

        log_button = Button(frame2, text = "LOG", command=logWindow)
        log_button.pack(side=LEFT)
        log_button.configure(state=DISABLED)
        self.log_button = log_button

        #Updateing status bar
        tasks_nr = 0.0
        for task in progress.to_do:
            tasks_nr = tasks_nr + task
        self.tasks_to_do = tasks_nr
        thread.start_new_thread(self.bar_update, ())
        self.bar_display(root)

        #Tooltips
        balloon.bind(exit_button, "Exit the Plugin")
        balloon.bind(save_button, "Save current project to tar.bz2 archive")
        balloon.bind(stop_button, "Cease calculations")
        balloon.bind(start_button, "Start/Resume calculations")

    ##This function will update status bar during molecular dynamics simulation (beware this is separate thread)
    def bar_update(self):
        percent = 0.0
        while stop == 1:
            time.sleep(0.5)
        while error == "" and percent != 100:
            time.sleep(0.5)
            percent = steps_status_bar("only_bar")
            self.queue_percent.put(percent)
            if stop == 0:
                self.queue_status.put(status[1])
            elif stop == 1:
                self.queue_status.put("User Stoped")
        if error != "":
            self.queue_status.put("Fatal Error")
            self.start_counting(0)
            self.start_button.configure(state=DISABLED)

    ##This function will update status bar in thread safe manner
    def bar_display(self, root):
        try:
            status = self.queue_status.get(block=False)
            self.bar_var.set(status)
        except Queue.Empty:
            status = "No change"
        try:
            percent = self.queue_percent.get(block=False)
            self.bar_widget.configure(value=percent)
        except:
            pass
        if status == "Fatal Error":
            root1 = Tk()
            root1.wm_title("GROMACS Error Message")
            frame = Frame(root1)
            frame.pack()
            w = Label(frame, text=error)
            w.pack()
            ok_button = Button(frame, text = "OK", command=root1.destroy)
            ok_button.pack()
            root1.mainloop()
        if status == "Finished!":
            root.destroy()
            #Show interpretation window after successful completion of the calculations...
            showInterpretationWindow()
        else:
            root.after(100, self.bar_display, root)

    ##This function will change global value if stop is clicked during simulation
    def start_counting(self, value):
        global stop
        if value == 1:
            stop = 0
            thread.start_new_thread(dynamics, ())
            self.stop_button.configure(state=ACTIVE)
            self.start_button.configure(state=DISABLED)
            self.log_button.configure(state=DISABLED)
        elif value == 0:
            stop = 1
            self.stop_button.configure(state=DISABLED)
            self.start_button.configure(state=ACTIVE)
            self.log_button.configure(state=ACTIVE)

##This window will allow to manipulate final molecule to interprate MD simulation results
class InterpretationWindow:

    dt = 0.0
    nsteps = 0.0
    nstxout = 0.0
    max_time = 0.0
    tentry_value = ""
    pause = 1

    def __init__(self):
        self.queue_time = Queue.Queue()
        self.md_time()
        root = Tk()
        self.window(root)
        root.mainloop()

    def md_time(self):
        md_file = open(project_dir+"md.mdp", "r")
        for lines in md_file.readlines():
            splited_line = lines.split(" ")
            if splited_line[0] == "dt":
                dt = float(splited_line[2])
                self.dt = dt
            elif splited_line[0] == "nsteps":
                nsteps = float(splited_line[2])
                self.nsteps = nsteps
            elif splited_line[0] == "nstxout":
                nstxout = float(splited_line[2])
                self.nstxout = nstxout
        max_time = dt * nsteps
        self.max_time = max_time

    def window(self, root):
        root.wm_title("MD Interpretation")
        self.tentry_value = StringVar(root)
        self.tentry_value.set("0.0")
        sentry_value = StringVar(root)
        sentry_value.set("1.0")
        contact_entry_value = StringVar(root)
        contact_entry_value.set("-1.0")

        frame1 = Frame(root)
        frame1.pack(side=TOP)

        #Animation
        alabel = Label(frame1, text="Animation", font = "bold")
        alabel.pack()
        frame1_1 = Frame(frame1)
        frame1_1.pack(side=TOP)
        play_button = Button(frame1_1, text = "PLAY", command=lambda : self.pause_play(0))
        play_button.pack(side=LEFT)
        pause_button = Button(frame1_1, text = "PAUSE", command=lambda : self.pause_play(1))
        pause_button.pack(side=LEFT)
        frame1_2 = Frame(frame1)
        frame1_2.pack(side=TOP, anchor=W)
        tlabel = Label(frame1_2, text="Time [ps] (Max "+str(self.max_time)+" [ps])")
        tlabel.pack(side=LEFT)
        tentry = Entry(frame1_2, textvariable=self.tentry_value)
        tentry.pack(side=LEFT)
        tok_button = Button(frame1_2, text = "OK", command=lambda : cmd.frame(self.time2frames(self.tentry_value.get()))) #PyMOL API
        tok_button.pack(side=LEFT)
        frame1_3 = Frame(frame1)
        frame1_3.pack(side=TOP, anchor=W)
        mlabel = Label(frame1_3, text="Model Type")
        mlabel.pack(side=LEFT)
        lines_button = Button(frame1_3, text = "Lines", command=lambda : self.shape("lines"))
        lines_button.pack(side=LEFT)
        sticks_button = Button(frame1_3, text = "Sticks", command=lambda : self.shape("sticks"))
        sticks_button.pack(side=LEFT)
        ribbon_button = Button(frame1_3, text = "Ribbon", command=lambda : self.shape("ribbon"))
        ribbon_button.pack(side=LEFT)
        cartoon_button = Button(frame1_3, text = "Cartoon", command=lambda : self.shape("cartoon"))
        cartoon_button.pack(side=LEFT)
        frame1_3_1 = Frame(frame1)
        frame1_3_1.pack(side=TOP, anchor=W)
        mlabel = Label(frame1_3_1, text="Labels")
        mlabel.pack(side=LEFT)
        end_button = Button(frame1_3_1, text = "Terminus", command=lambda : self.label("terminus"))
        end_button.pack(side=LEFT)
        acids_button = Button(frame1_3_1, text = "Amino Acids", command=lambda : self.label("acids"))
        acids_button.pack(side=LEFT)
        clear_button = Button(frame1_3_1, text = "Clear", command=lambda : self.label("clear"))
        clear_button.pack(side=LEFT)

        thread.start_new_thread(self.watch_frames, ())
        self.display_time(root)

        #Vectors
        vlabel = Label(frame1, text="Vectors (Require ProDy)", font = "bold")
        vlabel.pack()
        frame1_4 = Frame(frame1)
        frame1_4.pack(side=TOP, anchor=W)
        modlabel = Label(frame1_4, text="Mode Nr")
        modlabel.pack(side=LEFT)
        one_button = Button(frame1_4, text = "1", command=lambda : vectors_prody.change_vectors_mode_nr(0))
        one_button.pack(side=LEFT)
        two_button = Button(frame1_4, text = "2", command=lambda : vectors_prody.change_vectors_mode_nr(1))
        two_button.pack(side=LEFT)
        three_button = Button(frame1_4, text = "3", command=lambda : vectors_prody.change_vectors_mode_nr(2))
        three_button.pack(side=LEFT)
        frame1_5 = Frame(frame1)
        frame1_5.pack(side=TOP, anchor=W)
        slabel = Label(frame1_5, text="Scale")
        slabel.pack(side=LEFT)
        sentry = Entry(frame1_5, textvariable=sentry_value)
        sentry.pack(side=LEFT)
        sok_button = Button(frame1_5, text = "OK", command=lambda : vectors_prody.change_vectors_scale(sentry_value.get()))
        sok_button.pack(side=LEFT)
        frame1_6 = Frame(frame1)
        frame1_6.pack(side=TOP, anchor=W)
        modlabel = Label(frame1_6, text="Color")
        modlabel.pack(side=LEFT)
        gray_button = Button(frame1_6, text = "Gray", command=lambda : vectors_prody.change_vectors_color("gray"))
        gray_button.pack(side=LEFT)
        red_button = Button(frame1_6, text = "Red", command=lambda : vectors_prody.change_vectors_color("red"))
        red_button.pack(side=LEFT)
        blue_button = Button(frame1_6, text = "Blue", command=lambda : vectors_prody.change_vectors_color("blue"))
        blue_button.pack(side=LEFT)
        green_button = Button(frame1_6, text = "Green", command=lambda : vectors_prody.change_vectors_color("green"))
        green_button.pack(side=LEFT)

        frame1_7 = Frame(frame1)
        frame1_7.pack(side=TOP, anchor=W)
        modlabel = Label(frame1_7, text="Plot results")
        modlabel.pack(side=LEFT)
        contact_button = Button(frame1_7, text = "Show Contact Map Graph", command=lambda : vectors_prody.graph_contact_map("contact"))
        contact_button.pack(side=LEFT)
        cross_button = Button(frame1_7, text = "Show Cross-correlations Graph", command=lambda : vectors_prody.graph_contact_map("cross"))
        cross_button.pack(side=LEFT)
        frame1_8 = Frame(frame1)
        frame1_8.pack(side=TOP, anchor=W)
        modlabel = Label(frame1_8, text="Plot results")
        modlabel.pack(side=LEFT)
        contact_pymol_button = Button(frame1_8, text = "Show Contact Map In PyMOL", command=lambda : vectors_prody.show_contact_map(contact_entry_value.get()))
        contact_pymol_button.pack(side=LEFT)
        contact_label = Label(frame1_8, text="Sensitivity")
        contact_label.pack(side=LEFT)
        contact_entry = Entry(frame1_8, textvariable=contact_entry_value)
        contact_entry.pack(side=LEFT)

        frame1_8 = Frame(frame1)
        frame1_8.pack(side=TOP)
        exit_button = Button(frame1_8, text = "Exit", command=root.destroy)
        exit_button.pack(side=LEFT)
        save_button = Button(frame1_8, text = "Save", command=lambda : select_file_save(1))
        save_button.pack(side=LEFT)
        log_button = Button(frame1_8, text = "Log", command=logWindow)
        log_button.pack(side=LEFT)

        if prody_true != 1:
            print "No ProDy found"
            one_button.configure(state=DISABLED)
            two_button.configure(state=DISABLED)
            three_button.configure(state=DISABLED)
            sok_button.configure(state=DISABLED)
            gray_button.configure(state=DISABLED)
            red_button.configure(state=DISABLED)
            blue_button.configure(state=DISABLED)
            green_button.configure(state=DISABLED)
        if prody_true !=1 or vectors_prody.contact_map !=1:
            contact_button.configure(state=DISABLED)
            cross_button.configure(state=DISABLED)
            contact_pymol_button.configure(state=DISABLED)

    def pause_play(self, value):
        if value == 1:
            self.pause = 1
            cmd.mstop() #PyMOL API
        elif value == 0:
            self.pause = 0
            cmd.mplay() #PyMOL API

    def frames2time(self, text_var):
        frame = float(text_var)
        time = frame * self.dt * self.nstxout
        return time

    def time2frames(self, text_var):
        nsecond = float(text_var)
        frame = nsecond / self.dt / self.nstxout    
        frame = int(frame)
        return frame

    def shape(self, shape_type):
        cmd.hide("everything", project_name+"_multimodel") #PyMOL API
        cmd.show(shape_type, project_name+"_multimodel") #PyMOL API

    def label(self, name):
        if name == "terminus":
            cmd.label("n. ca and "+project_name+"_multimodel and i. 1", '"N-terminus"') #PyMOL API
            ca_number = cmd.count_atoms("n. ca and "+project_name+"_multimodel") #PyMOL API
            cmd.label("n. ca and "+project_name+"_multimodel and i. " + str(ca_number), '"C-terminus"') #PyMOL API
        elif name == "acids":
            cmd.label("n. ca and "+project_name+"_multimodel", "resn") #PyMOL API
        elif name == "clear":
            cmd.label("n. ca and "+project_name+"_multimodel", "") #PyMOL API

    ##This function will watch time (beware this is separate thread)
    def watch_frames(self):
        while 1:
            pymol_frame = cmd.get_frame() #PyMOL API
            pymol_time = self.frames2time(pymol_frame)
            self.queue_time.put(pymol_time)
            time.sleep(0.1)

    ##This function will update display time in thread safe manner
    def display_time(self, root):
        try:
            time = self.queue_time.get(block=False)
        except Queue.Empty:
            time = "No change"
        if self.pause != 1:
            self.tentry_value.set(time)
        root.after(100, self.display_time, root)

## Show interpretation window...
def showInterpretationWindow():
    interpretation = InterpretationWindow()
    try:
        interpretation()
    except AttributeError:
        pass

##Gather all water options windows in one class
class WaterWindows:

    implicit_buttons = []
    explicit_buttons = []

    ##Water chooser window
    def choose(self, v4_water, water_v, waterbox_button, master):
        root = Toplevel(master)
        root.wm_title("Water Model")

        v1 = IntVar(root)
        v1.set(gromacs2.explicit)

        v2 = IntVar(root)
        v2.set(0)

        radio_button2 = Radiobutton(root, text="Explicit Solvent Simulation", value=1, variable=v1, command = lambda : self.change_e(v1.get(), v4_water, water_v, v2))
        radio_button2.pack(side=TOP, anchor=W)

        frame1 = Frame(root, padx=10)
        frame1.pack(anchor=W)

        self.explicit_buttons = []

        for water in gromacs.water_list:
            radio_button1 = Radiobutton(frame1, text=water[1], value=water[0], variable=v4_water, command = lambda : self.change(v4_water, water_v))
            radio_button1.pack(side=TOP, anchor=W)
            self.explicit_buttons.append(radio_button1)
        self.explicit_buttons.append(waterbox_button)

        radio_button2 = Radiobutton(root, text="Implicit Solvent Simulation", value=0, variable=v1, command = lambda : self.change_e(v1.get(), v4_water, water_v, v2))
        radio_button2.pack(side=TOP, anchor=W)

        frame2 = Frame(root, padx=10)
        frame2.pack(anchor=W)
        radio_button3_1 = Radiobutton(frame2, text="Still", value=0, variable=v2, command = lambda : self.change_i(v2))
        radio_button3_1.pack(side=TOP, anchor=W)
        radio_button3_2 = Radiobutton(frame2, text="Hawkins-Cramer-Truhlar", value=1, variable=v2, command = lambda : self.change_i(v2))
        radio_button3_2.pack(side=TOP, anchor=W)
        radio_button3_3 = Radiobutton(frame2, text="Onufriev-Bashford-Case", value=2, variable=v2, command = lambda : self.change_i(v2))
        radio_button3_3.pack(side=TOP, anchor=W)

        self.implicit_buttons = [radio_button3_1, radio_button3_2, radio_button3_3]
        self.change_e(gromacs2.explicit, v4_water, water_v, v2)

        ok_button = Button(root, text = "OK", command=root.destroy)
        ok_button.pack(side=TOP)

    ##This function will change force field and water model when choosing Force Field in Main Window and also change water model after choosing one in "waterChoose"
    def change(self, v4_water, water_v, force = ""):
        if force == "":
            force = gromacs2.force
        else:
            gromacs2.force = force
        gromacs.water_update(force)
        if gromacs2.explicit == 1:
            water_v.set(gromacs.water_list[v4_water.get()-1][1])
        elif gromacs2.explicit == 0:
            water_v.set("Implicit Solvent")
        gromacs2.water = v4_water.get()

    ##This function changes explicit to implicit and vice versa water model
    def change_e(self, value, v4_water, water_v, v2):
        gromacs2.update({"explicit" : value})
        if gromacs2.explicit == 1:
            for button in self.implicit_buttons:
                button.configure(state=DISABLED)
            for button in self.explicit_buttons:
                button.configure(state=ACTIVE)
            progress.to_do[2] = 1
            progress.to_do[3] = 1
            progress.to_do[5] = 1
            #em update
            if not os.path.isfile(dynamics_dir + "em.mdp"):
                parameter_nr = 0
                for parameter in em_file.options:
                    if (parameter[0] == "rlist") or (parameter[0] == ";rlist"):
                        em_file.update(parameter_nr, "1.0")
                    elif (parameter[0] == "rcoulomb") or (parameter[0] == ";rcoulomb"):
                        em_file.update(parameter_nr, "1.0")
                    elif (parameter[0] == "rvdw") or (parameter[0] == ";rvdw"):
                        em_file.update(parameter_nr, "1.0")
                    elif (parameter[0] == "implicit-solvent") or (parameter[0] == ";implicit-solvent"):
                        em_file.update(parameter_nr, "no")
                    elif (parameter[0] == "pbc") or (parameter[0] == ";pbc"):
                        em_file.update(parameter_nr, "no", 0)
                    elif (parameter[0] == "rgbradii") or (parameter[0] == ";rgbradii"):
                        em_file.update(parameter_nr, "0", 0)
                    elif (parameter[0] == "cutoff-scheme") or (parameter[0] == ";cutoff-scheme"):
                        em_file.update(parameter_nr, "Verlet")
                    elif (parameter[0] == "coulombtype") or (parameter[0] == ";coulombtype"):
                        em_file.update(parameter_nr, "PME")
                    parameter_nr = parameter_nr + 1
            #md update
            if not os.path.isfile(dynamics_dir + "md.mdp"):
                parameter_nr = 0
                for parameter in md_file.options:
                    if (parameter[0] == "nstlist") or (parameter[0] == ";nstlist"):
                        md_file.update(parameter_nr, "10")
                    elif (parameter[0] == "rlist") or (parameter[0] == ";rlist"):
                        md_file.update(parameter_nr, "1.0")
                    elif (parameter[0] == "rcoulomb") or (parameter[0] == ";rcoulomb"):
                        md_file.update(parameter_nr, "1.0")
                    elif (parameter[0] == "rvdw") or (parameter[0] == ";rvdw"):
                        md_file.update(parameter_nr, "1.0")
                    elif (parameter[0] == "Tcoupl") or (parameter[0] == ";Tcoupl"):
                        md_file.update(parameter_nr, "v-rescale")
                    elif (parameter[0] == "tau_t") or (parameter[0] == ";tau_t"):
                        md_file.update(parameter_nr, "0.1 0.1")
                    elif (parameter[0] == "tc-grps") or (parameter[0] == ";tc-grps"):
                        md_file.update(parameter_nr, "protein Non-Protein")
                    elif (parameter[0] == "ref_t") or (parameter[0] == ";ref_t"):
                        md_file.update(parameter_nr, "298 298")
                    elif (parameter[0] == "implicit-solvent") or (parameter[0] == ";implicit-solvent"):
                        md_file.update(parameter_nr, "no")
                    elif (parameter[0] == "pbc") or (parameter[0] == ";pbc"):
                        md_file.update(parameter_nr, "no", 0)
                    elif (parameter[0] == "rgbradii") or (parameter[0] == ";rgbradii"):
                        md_file.update(parameter_nr, "0", 0)
                    elif (parameter[0] == "comm_mode") or (parameter[0] == ";comm_mode"):
                        md_file.update(parameter_nr, "ANGULAR", 0)
                    elif (parameter[0] == "cutoff-scheme") or (parameter[0] == ";cutoff-scheme"):
                        md_file.update(parameter_nr, "Verlet")
                    elif (parameter[0] == "coulombtype") or (parameter[0] == ";coulombtype"):
                        md_file.update(parameter_nr, "PME")
                    parameter_nr = parameter_nr + 1
        elif gromacs2.explicit == 0:
            for button in self.implicit_buttons:
                button.configure(state=ACTIVE)
            for button in self.explicit_buttons:
                button.configure(state=DISABLED)
            progress.to_do[2] = 0
            progress.to_do[3] = 0
            progress.to_do[5] = 0
            #em update
            if not os.path.isfile(dynamics_dir + "em.mdp"):
                parameter_nr = 0
                for parameter in em_file.options:
                    if (parameter[0] == "rlist") or (parameter[0] == ";rlist"):
                        em_file.update(parameter_nr, "0")
                    elif (parameter[0] == "rcoulomb") or (parameter[0] == ";rcoulomb"):
                        em_file.update(parameter_nr, "0")
                    elif (parameter[0] == "rvdw") or (parameter[0] == ";rvdw"):
                        em_file.update(parameter_nr, "0")
                    elif (parameter[0] == "implicit-solvent") or (parameter[0] == ";implicit-solvent"):
                        em_file.update(parameter_nr, "GBSA")
                    elif (parameter[0] == "pbc") or (parameter[0] == ";pbc"):
                        em_file.update(parameter_nr, "no")
                    elif (parameter[0] == "rgbradii") or (parameter[0] == ";rgbradii"):
                        em_file.update(parameter_nr, "0")
                    elif (parameter[0] == "cutoff-scheme") or (parameter[0] == ";cutoff-scheme"):
                        em_file.update(parameter_nr, "group")
                    elif (parameter[0] == "coulombtype") or (parameter[0] == ";coulombtype"):
                        em_file.update(parameter_nr, "Cut-off")
                    parameter_nr = parameter_nr + 1
            #md update
            if not os.path.isfile(dynamics_dir + "md.mdp"):
                parameter_nr = 0
                for parameter in md_file.options:
                    if (parameter[0] == "nstlist") or (parameter[0] == ";nstlist"):
                        md_file.update(parameter_nr, "0")
                    elif (parameter[0] == "rlist") or (parameter[0] == ";rlist"):
                        md_file.update(parameter_nr, "0")
                    elif (parameter[0] == "rcoulomb") or (parameter[0] == ";rcoulomb"):
                        md_file.update(parameter_nr, "0")
                    elif (parameter[0] == "rvdw") or (parameter[0] == ";rvdw"):
                        md_file.update(parameter_nr, "0")
                    elif (parameter[0] == "Tcoupl") or (parameter[0] == ";Tcoupl"):
                        md_file.update(parameter_nr, "berendsen", 0)
                    elif (parameter[0] == "tau_t") or (parameter[0] == ";tau_t"):
                        md_file.update(parameter_nr, "0.1 0.1", 0)
                    elif (parameter[0] == "tc-grps") or (parameter[0] == ";tc-grps"):
                        md_file.update(parameter_nr, "protein Non-Protein", 0)
                    elif (parameter[0] == "ref_t") or (parameter[0] == ";ref_t"):
                        md_file.update(parameter_nr, "298 298", 0)
                    elif (parameter[0] == "implicit-solvent") or (parameter[0] == ";implicit-solvent"):
                        md_file.update(parameter_nr, "GBSA")
                    elif (parameter[0] == "pbc") or (parameter[0] == ";pbc"):
                        md_file.update(parameter_nr, "no")
                    elif (parameter[0] == "rgbradii") or (parameter[0] == ";rgbradii"):
                        md_file.update(parameter_nr, "0")
                    elif (parameter[0] == "comm_mode") or (parameter[0] == ";comm_mode"):
                        md_file.update(parameter_nr, "ANGULAR")
                    elif (parameter[0] == "cutoff-scheme") or (parameter[0] == ";cutoff-scheme"):
                        md_file.update(parameter_nr, "group")
                    elif (parameter[0] == "coulombtype") or (parameter[0] == ";coulombtype"):
                        md_file.update(parameter_nr, "Cut-off")
                    parameter_nr = parameter_nr + 1
            self.change_i(v2)
            #in implicit solvent watermodel must be set to "None"
            v4_water.set(len(self.explicit_buttons) - 1)

        self.change(v4_water, water_v)

    ##This function changes implicit water model
    def change_i(self, int_variable):
        if int_variable.get() == 0:
            if not os.path.isfile(dynamics_dir + "em.mdp"):
                parameter_nr = 0
                for parameter in em_file.options:
                    if (parameter[0] == "gb-algorithm") or (parameter[0] == ";gb-algorithm"):
                        em_file.update(parameter_nr, "Still")
                    parameter_nr = parameter_nr + 1
            if not os.path.isfile(dynamics_dir + "md.mdp"):
                parameter_nr = 0
                for parameter in md_file.options:
                    if (parameter[0] == "gb-algorithm") or (parameter[0] == ";gb-algorithm"):
                        md_file.update(parameter_nr, "Still")
                    parameter_nr = parameter_nr + 1
        elif int_variable.get() == 1:
            if not os.path.isfile(dynamics_dir + "em.mdp"):
                parameter_nr = 0
                for parameter in em_file.options:
                    if (parameter[0] == "gb-algorithm") or (parameter[0] == ";gb-algorithm"):
                        em_file.update(parameter_nr, "HCT")
                    parameter_nr = parameter_nr + 1
            if not os.path.isfile(dynamics_dir + "md.mdp"):
                parameter_nr = 0
                for parameter in md_file.options:
                    if (parameter[0] == "gb-algorithm") or (parameter[0] == ";gb-algorithm"):
                        md_file.update(parameter_nr, "HCT")
                    parameter_nr = parameter_nr + 1
        elif int_variable.get() == 2:
            if not os.path.isfile(dynamics_dir + "em.mdp"):
                parameter_nr = 0
                for parameter in em_file.options:
                    if (parameter[0] == "gb-algorithm") or (parameter[0] == ";gb-algorithm"):
                        em_file.update(parameter_nr, "OBC")
                    parameter_nr = parameter_nr + 1
            if not os.path.isfile(dynamics_dir + "md.mdp"):
                parameter_nr = 0
                for parameter in md_file.options:
                    if (parameter[0] == "gb-algorithm") or (parameter[0] == ";gb-algorithm"):
                        md_file.update(parameter_nr, "OBC")
                    parameter_nr = parameter_nr + 1

    ##Water box configuration window
    def box(self, master):
        root = Toplevel(master)
        root.wm_title("Water Box Options")
        root.wm_geometry("300x200")
        v = StringVar(root)
        v.set(gromacs2.box_type)
        w = Label(root, text="Box type")
        w.pack()
        radio_button = Radiobutton(root, text="triclinic", value="triclinic", variable=v, command = lambda : gromacs2.update({"box_type" : v.get()}))
        radio_button.pack(side=TOP, anchor=W)
        radio_button = Radiobutton(root, text="cubic", value="cubic", variable=v, command = lambda : gromacs2.update({"box_type" : v.get()}))
        radio_button.pack(side=TOP, anchor=W)
        radio_button = Radiobutton(root, text="dodecahedron", value="dodecahedron", variable=v, command = lambda : gromacs2.update({"box_type" : v.get()}))
        radio_button.pack(side=TOP, anchor=W)
        radio_button = Radiobutton(root, text="octahedron", value="octahedron", variable=v, command = lambda : gromacs2.update({"box_type" : v.get()}))
        radio_button.pack(side=TOP, anchor=W)
        w1 = Label(root, text="Distance")
        w1.pack()
        distance = Entry(root)
        distance.pack(side=TOP)
        distance.insert(0, gromacs2.box_distance)
        w2 = Label(root, text="Density [g/L]")
        w2.pack()
        density = Entry(root)
        density.pack(side=TOP)
        density.insert(0, gromacs2.box_density)
        ok_button = Button(root, text = "OK", command=lambda : gromacs2.update({"box_distance" : distance.get(), "box_density" : density.get()}, root))
        ok_button.pack(side=TOP)

    ##Hydrogen configuration (for bigger time steps)
    def box2(self, master):
        root = Toplevel(master)
        root.wm_title("Hydrogen options (for Pdb2gmx)")
        root.wm_geometry("300x200") 
        v1 = StringVar (root)
        v1.set(gromacs2.hydro)
        w = Label(root, text="Hydrogen type (for pdb2gmx only)")
        w.pack()
        radio_button = Radiobutton(root, text="Normal Hydrogen", value="noheavyh", variable=v1, command = lambda : gromacs2.update({"hydro" : v1.get()}))
        radio_button.pack(side=TOP, anchor=W)
        radio_button = Radiobutton(root, text="Deuterium", value="deuterate", variable=v1, command = lambda : gromacs2.update({"hydro" : v1.get()}))
        radio_button.pack(side=TOP, anchor=W)
        radio_button = Radiobutton(root, text="Heavy Hydrogen (4amu) ", value="heavyh", variable=v1, command = lambda : gromacs2.update({"hydro" : v1.get()}))
        radio_button.pack(side=TOP, anchor=W)
        ok_button = Button(root, text = "OK", command=root.destroy)
        ok_button.pack(side=TOP)

# Options for the genion class all the options
class GenionWindow:

    ##Genion box configuration window
    def window(self, master):
        root = Toplevel(master)
        root.wm_title("GENION options")
        root.wm_geometry("300x350")
        v = StringVar(root)
        v.set(gromacs2.neutrality)
        w = Label(root, text="Parameters for genion")
        w.pack()
        radio_button = Radiobutton(root, text="Neutralize System", value="neutral", variable=v, command = lambda : gromacs2.update({"neutrality" : v.get()}))
        radio_button.pack(side=TOP, anchor=W)
        radio_button = Radiobutton(root, text="Do not Neutralize", value="noneutral", variable=v, command = lambda : gromacs2.update({"neutrality" : v.get()}))
        radio_button.pack(side=TOP, anchor=W)
        w1 = Label(root, text="Salt Concentration")
        w1.pack()
        salt = Entry(root)
        salt.pack(side=TOP)
        salt.insert(0, gromacs2.salt_conc)
        w2 = Label(root, text="Positive Ion")
        w2.pack()
        posit = Entry(root)
        posit.pack(side=TOP)
        posit.insert(0, gromacs2.positive_ion)
        w3 = Label(root, text="Negative Ion")
        w3.pack()
        negat = Entry(root)
        negat.pack(side=TOP)
        negat.insert(0, gromacs2.negative_ion)
        ok_button = Button(root, text = "OK", command=lambda : gromacs2.update({"salt_conc" : salt.get(), "positive_ion" : posit.get(), "negative_ion" : negat.get()}, root))
        ok_button.pack(side=TOP)

##This class is resposible for graphic edition of restraints
class RestraintsWindow:

    atom_list = []
    check_var = ""

    ##This function will create main window for restraints
    def window(self, master):
        root = Toplevel(master)
        root.wm_title("Restraints Configure")

        ok_button = Button(root, text="OK", command=lambda : self.index(root))
        ok_button.pack(side=BOTTOM)

        sb = Scrollbar(root, orient=VERTICAL)
        sb.pack(side=RIGHT, fill=Y)

        canvas = Canvas(root, width=600)
        canvas.pack(side=TOP, fill="both", expand=True)
        frame1 = Frame(canvas)
        frame1.pack(side=TOP)

        #attach canvas (with frame1 in it) to scrollbar
        canvas.config(yscrollcommand=sb.set)
        sb.config(command=canvas.yview)

        #bind frame1 with canvas
        canvas.create_window((1,1), window=frame1, anchor="nw", tags="frame1")
        frame1.bind("<Configure>", canvas.config(scrollregion=(0, 0, 0, 4500)))

        self.check_var = IntVar(frame1)
        self.check_var.set(gromacs2.restraints_nr)

        self.atom_list = []
        number = 0
        for group in gromacs.restraints:
            select = Radiobutton(frame1, text=group[0], value=number, variable=self.check_var)
            select.pack()
            text = Text(frame1)
            text.insert(END, group[1])
            text.pack()
            self.atom_list.append(text)
            number = number + 1

        select1 = Radiobutton(frame1, text="[ PyMol Selected ]", value=number, variable=self.check_var)
        select1.pack()
        text1 = Text(frame1)

        stored.list=[]
        cmd.iterate("(sele)","stored.list.append(ID)") #PyMOL API

        stored_string = ""
        for atom in stored.list:
            stored_string = stored_string + str(atom)
            lengh = stored_string.split('\n')
            if len(lengh[-1]) < 72:
                stored_string = stored_string + "   "
            else:
                stored_string = stored_string + "\n"

        text1.insert(END, stored_string)
        text1.pack()
        self.atom_list.append(text1)

    ##This function will modyfie index_dynamics.ndx file based on user choosed restraints       
    def index(self, root_to_kill=""):
        index_nr = self.check_var.get()
        gromacs2.restraints_nr = index_nr
        text = self.atom_list[index_nr]
        if index_nr < len(gromacs.restraints):
            gromacs.restraints[index_nr][1] = text.get(1.0, END)
            gromacs.restraints = gromacs.restraints
        index_file = open("index_dynamics.ndx", "w")
        index_file.write("[ Dynamics Selected ]\n"+text.get(1.0, END))
        index_file.close()
        if root_to_kill != "":
            root_to_kill.destroy()

    ##This function will activ or disable restraints button in main window based on check box
    def check(self, check, config_button):
        global md_file, progress
        if check == 1:
            config_button.configure(state=ACTIVE)
            md_file.update(2, md_file.options[2][1], 1)
            gromacs.restraints_index()
            progress.to_do[6] = 1
            progress.to_do = progress.to_do
        elif check == 0:
            config_button.configure(state=DISABLED)
            md_file.update(2, md_file.options[2][1], 0)
            progress.to_do[6] = 0
            progress.to_do = progress.to_do

##This function will create window, which allow you to choose PDB file if no file is loaded to PyMOL
def select_file(v_name):
    root = Tk()
    file = tkFileDialog.askopenfile(parent=root, mode='rb',title='Choose PDB file')
    try:
        name = file.name.split("/")
        name2 = name[-1].split(".")
        ##Checking directories
        global project_name, project_dir
        project_name = name2[0]
        setGromacsProjectDir()
        v_name.set(project_name)
        if os.path.isdir(project_dir) == False:
            os.makedirs(project_dir)
            shutil.copyfile(file.name, project_dir + project_name + ".pdb")
            print "pdb_copied"
        create_config_files()   
    except:
        pass
    root.destroy()

##This function will create window, which allow you to save current work
def select_file_save(rest_of_work=0):
    if project_name != "nothing":
        if rest_of_work == 1:
            progress.to_do_status()
        root = Tk()
        file = tkFileDialog.asksaveasfile(parent=root, mode='w' ,title='Choose save file')
        if file != None:
            save_file(file.name)    
        root.destroy()
    elif project_name == "nothing":
        no_molecule_warning()

##This function will create window, which allow you to load previously saved work
def select_file_load(frame1_1a, v1_name, v2_group, v3_force, v4_water, water_v, config_button_restraints):
    root = Tk()
    file = tkFileDialog.askopenfile(parent=root, mode='rb', defaultextension=".tar.bz2" ,title='Choose file to load')
    if file != None:
        load_file(file.name)
        v1_name.set(project_name)
        v2_group.set(gromacs.group_list[gromacs2.group][0])
        v3_force.set(gromacs.force_list[gromacs2.force-1][0])
        v4_water.set(gromacs.water_list[gromacs2.water-1][0])
        water_v.set(gromacs.water_list[v4_water.get()-1][1])
        radio_button1 = Radiobutton(frame1_1a, text=project_name, value=project_name, variable=v1_name, command=lambda: set_variables(v1_name.get(), v2_group, v3_force, v4_water, water_v, config_button_restraints, prody_button))
        radio_button1.pack(side=TOP, anchor=W)
    root.destroy()

##This function sets variables after choosing new molecule
def set_variables(name, v2_group, v3_force, v4_water, water_v, config_button_restraints):
    print "Set Variables"
    ##Set project name and dir
    if name != "":
        global project_name, project_dir
        project_name = name
        setGromacsProjectDir()
    if os.path.isfile(project_dir+"options.pickle") == True:
        load_options()
        v2_group.set(gromacs.group_list[gromacs2.group][0])
        v3_force.set(gromacs.force_list[gromacs2.force-1][0])
        v4_water.set(gromacs.water_list[gromacs2.water-1][0])
        water_v.set(gromacs.water_list[v4_water.get()-1][1])
    else:
        create_config_files()
    ##Correct set of restraints button
    if progress.to_do[6] == 0:
        config_button_restraints.configure(state=DISABLED)
    elif progress.to_do[6] == 1:
        config_button_restraints.configure(state=ACTIVE)
    ##If Resume is zero than initial Steps are all ON
    if progress.resume == 0:
        progress.to_do = [1,1,1,1,1,1,0,1,1,1]

##This function creates files needed by the project
def create_config_files():
    print "Create config files"
    global em_file, pr_file, md_file, progress
    if not os.path.isfile(project_dir + "options.pickle"):
        progress = Progress_status()
    else:
        load_options()
    if os.path.isfile(dynamics_dir + "em.mdp"):
        shutil.copy(dynamics_dir + "em.mdp", project_dir + "em.mdp")
        print "Found em.mdp file. Using it instead of local configuration."
    elif os.path.isfile(project_dir + "em.mdp"):
        em_file_config = open(project_dir + "em.mdp", "r").read()
        em_file = Mdp_config("em.mdp",em_file_config, 1)
    else:
        em_file = Mdp_config("em.mdp",em_init_config, 0)
    if os.path.isfile(dynamics_dir + "pr.mdp"):
        shutil.copy(dynamics_dir + "pr.mdp", project_dir + "pr.mdp")
        print "Found pr.mdp file. Using it instead of local configuration."
    elif os.path.isfile(project_dir + "pr.mdp"):
        pr_file_config = open(project_dir + "pr.mdp", "r").read()
        pr_file = Mdp_config("pr.mdp",pr_file_config, 1)
    else:
        pr_file = Mdp_config("pr.mdp",pr_init_config, 0)
    if os.path.isfile(dynamics_dir + "md.mdp"):
        shutil.copy(dynamics_dir + "md.mdp", project_dir + "md.mdp")
        print "Found md.mdp file. Using it instead of local configuration."
    elif os.path.isfile(project_dir + "md.mdp"):
        md_file_config = open(project_dir + "md.mdp", "r").read()
        md_file = Mdp_config("md.mdp",md_file_config, 1)
    else:
        md_file = Mdp_config("md.mdp",md_init_config, 0)
    save_options()
    if project_name in cmd.get_names("objects"): #PyMOL API
        cmd.save(project_dir+project_name+".pdb", project_name) #PyMOL API
        print "cmd saved"

#This function will create the window with configuration files based on MDP class
def mdp_configure(config_name, master):
    if project_name != "nothing":
        root2 = Toplevel(master)

        if config_name == "em":
            em_file.clean_artefacts()
            options = em_file.options
            root2.wm_title("Energy Minimization Options")
        elif config_name == "pr":
            pr_file.clean_artefacts()
            options = pr_file.options
            root2.wm_title("Position Restrained MD Options")
        elif config_name == "md":
            md_file.clean_artefacts()
            options = md_file.options
            root2.wm_title("Molecular Dynamics Simulation Options")

        values_list = []
        check_list = []

        if config_name == "em":
            b = Button(root2, text="OK", command=lambda: mdp_update(values_list, check_list, "em", root2))
            b.pack(side=BOTTOM)
        elif config_name == "pr":
            b = Button(root2, text="OK", command=lambda: mdp_update(values_list, check_list, "pr", root2))
            b.pack(side=BOTTOM)
        elif config_name == "md":
            b = Button(root2, text="OK", command=lambda: mdp_update(values_list, check_list, "md", root2))
            b.pack(side=BOTTOM)

        sb = Scrollbar(root2, orient=VERTICAL)
        sb.pack(side=RIGHT, fill=Y)

        canvas = Canvas(root2, width=400)
        canvas.pack(side=TOP, fill="both", expand=True)
        frame1 = Frame(canvas)
        frame1.pack(side=TOP)

        #attach canvas (with frame1 in it) to scrollbar
        canvas.config(yscrollcommand=sb.set)
        sb.config(command=canvas.yview)

        #bind canvas with frame1 1/2
        canvas.create_window((1,1), window=frame1, anchor="nw", tags="frame1")
        for option, value in options:
            frame2 = Frame(frame1)
            frame2.pack(side=TOP)
            if option == "emtol":
                l1 = Label(frame2, text="Energy minimizing stuff")
                l1.pack(side=TOP)
            elif option == "Tcoupl":
                l1 = Label(frame2, text="Berendsen temperature and coupling")
                l1.pack(side=TOP)
            elif option == "Pcoupl":
                l1 = Label(frame2, text="Pressure coupling")
                l1.pack(side=TOP)
            elif option == "gen_vel":
                l1 = Label(frame2, text="Generate velocites temperature")
                l1.pack(side=TOP)
            elif option == "constraints":
                l1 = Label(frame2, text="Options for bonds")
                l1.pack(side=TOP)
            values_list.append(StringVar(root2))
            values_list[-1].set(value)
            check_list.append(IntVar(root2))
            if option[0] != ";":
                check_list[-1].set(1)
                c1 = Checkbutton(frame2, text=option, variable=check_list[-1], width=25, anchor=W)
                c1.pack(side=LEFT)
            else:
                check_list[-1].set(0)
                c1 = Checkbutton(frame2, text=option, variable=check_list[-1], width=25, anchor=W)
                c1.pack(side=LEFT)
            e = Entry(frame2, textvariable=values_list[-1])
            e.pack(side=LEFT)

        #bind canvas with frame1 2/2
        frame1.bind("<Configure>", canvas.config(scrollregion=(0, 0, 0, len(values_list)*25)))

    elif project_name == "nothing":
        no_molecule_warning()

##This function will update MDP class objects alfter closing "mdp_configure" window
def mdp_update(values, check_list, mdp, root_to_kill=""):
    try:
        root_to_kill.destroy()
    except:
        pass
    index_nr = 0
    for value in values:
        if mdp == "em":
            em_file.update(index_nr, value.get(), check_list[index_nr].get())
        elif mdp == "pr":
            pr_file.update(index_nr, value.get(), check_list[index_nr].get())
        elif mdp == "md":
            md_file.update(index_nr, value.get(), check_list[index_nr].get())
        index_nr = index_nr + 1
    save_options()

##This function will create Simulation Steps configuration window
def steps_configure(master, restraints_button):
    if project_name != "nothing":
        root = Toplevel(master)
        root.wm_title("Simulation Steps Configuration")
        check_var1 = IntVar(root)
        check_var1.set(progress.to_do[0])
        check_var2 = IntVar(root)
        check_var2.set(progress.to_do[1])
        v1 = IntVar(root)
        v1.set(progress.x2top)
        check_var3 = IntVar(root)
        check_var3.set(progress.to_do[2])
        #Created empty variable check_var4 for genion
        check_var4 = IntVar(root)
        check_var4.set(progress.to_do[3])
        check_var5 = IntVar(root)
        check_var5.set(progress.to_do[4])
        check_var6 = IntVar(root)
        check_var6.set(progress.to_do[5])
        check_var7 = IntVar(root)
        check_var7.set(progress.to_do[6])
        check_var8 = IntVar(root)
        check_var8.set(progress.to_do[7])
        check_var9 = IntVar(root)
        check_var9.set(progress.to_do[8])
        check_var10 = IntVar(root)
        check_var10.set(progress.to_do[9])
        #Variable for Resume Simulation
        check_var11 = IntVar(root)
        check_var11.set(progress.resume)

        frame1 = Frame(root)
        frame1.pack(side=TOP)

        c1 = Checkbutton(frame1, text="Save configuration files"+steps_status_done(0), variable=check_var1, command=lambda: progress.to_do_update(0, check_var1.get()))
        c1.pack(side=TOP, anchor=W)

        c2 = Checkbutton(frame1, text="Generate topology file from pdb"+steps_status_done(1), variable=check_var2, command=lambda: progress.to_do_update(1, check_var2.get()))
        c2.pack(side=TOP, anchor=W)

        r1 = Radiobutton(frame1, text="Use pdb2gmx tool", value=0, variable=v1, command=lambda: progress.x2top_update(v1.get()))
        r1.pack(side=TOP, anchor=W)

        r2 = Radiobutton(frame1, text="Use x2top tool", value=1, variable=v1, command=lambda: progress.x2top_update(v1.get()))
        r2.pack(side=TOP, anchor=W)

        c3 = Checkbutton(frame1, text="Adding Water Box (only for explicit solvent)"+steps_status_done(2), variable=check_var3, command=lambda: progress.to_do_update(2, check_var3.get()))
        c3.pack(side=TOP, anchor=W)

        c4 = Checkbutton(frame1, text="Adding ions and neutralize (only for explicit solvent; Optional)"+steps_status_done(3), variable=check_var4, command=lambda: progress.to_do_update(3, check_var4.get()))
        c4.pack(side=TOP, anchor=W)

        c5 = Checkbutton(frame1, text="Energy Minimization (optional)"+steps_status_done(4), variable=check_var5, command=lambda: progress.to_do_update(4, check_var5.get()))
        c5.pack(side=TOP, anchor=W)

        c6 = Checkbutton(frame1, text="Position Restrained MD (optional, only for explicit solvent)"+steps_status_done(5), variable=check_var6, command=lambda: progress.to_do_update(5, check_var6.get()))
        c6.pack(side=TOP, anchor=W)

        c7 = Checkbutton(frame1, text="Restraints (optional)"+steps_status_done(6), variable=check_var7, command=lambda: restraintsW.check(check_var7.get(), restraints_button))
        c7.pack(side=TOP, anchor=W)

        c8 = Checkbutton(frame1, text="Molecular Dynamics Simulation"+steps_status_done(7), variable=check_var8, command=lambda: progress.to_do_update(7, check_var8.get()))
        c8.pack(side=TOP, anchor=W)

        c9 = Checkbutton(frame1, text="Generate multimodel PDB"+steps_status_done(8), variable=check_var9, command=lambda: progress.to_do_update(8, check_var9.get()))
        c9.pack(side=TOP, anchor=W)

        c10 = Checkbutton(frame1, text="Calculate vectors using ProDy (optional)"+steps_status_done(9), variable=check_var10, command=lambda: progress.to_do_update(9, check_var10.get()))
        c10.pack(side=TOP, anchor=W)

        if prody_true != 1:
            check_var11.set(0)
            c10.configure(state=DISABLED)
            progress.to_do_update(9, 0)

        if gromacs2.explicit !=1:
            check_var3.set(0)
            c3.configure(state=DISABLED)
            progress.to_do_update(2, 0)
            check_var4.set(0)
            c4.configure(state=DISABLED)
            progress.to_do_update(3, 0)
            check_var6.set(0)
            c6.configure(state=DISABLED)
            progress.to_do_update(5, 0)

        l1 = Label(frame1, text="Simulation Progress:")
        l1.pack(side=TOP)

        variable_list = [check_var1, check_var2, check_var3, check_var4, check_var5, check_var6, check_var7, check_var8, check_var9, check_var10, check_var11]
        progress_bar = Progressbar(frame1)
        progress_bar.pack(side=TOP)
        if check_var11.get() == 1:
            percent = steps_status_bar(check_var11.get(), variable_list)
            progress_bar.configure(value=percent)

        c11 = Checkbutton(frame1, text="Resume Simulation", variable=check_var11, command=lambda: steps_click_resume(check_var11.get(), progress_bar, variable_list))
        c11.pack(side=TOP, anchor=W)

        b1 = Button(root, text="OK", command=lambda: steps_click_ok (root))
        b1.pack(side=TOP)
    elif project_name == "nothing":
        no_molecule_warning()

##This function will update status bar if checkbutton is clicked
def steps_click_resume(var, bar, variable_list=[]):
    percent = steps_status_bar(var, variable_list)
    bar.configure(value=percent)

##This function will close steps window and update number of steps to do
def steps_click_ok (root):
    root.destroy()
    progress.steps = sum(progress.to_do)

##This function will show current progress on Progress Bar and operate with Steps Simulation Window for "Resume Simulation" button.
def steps_status_bar(var, variable_list=[]):
    percent = 0.0
    if var == 1:
        to_do_nr = 0
        for step in progress.status:
            if step == 1:
                progress.to_do[to_do_nr] = 0
                progress.to_do = progress.to_do
                variable_list[to_do_nr].set(0)
            elif step == 0 and to_do_nr != 6:
                progress.to_do[to_do_nr] = 1
                progress.to_do = progress.to_do
                variable_list[to_do_nr].set(1)
            to_do_nr = to_do_nr + 1
        progress.resume = 1
    elif var == 0:
        percent = 0.0
        progress.to_do = [1,1,1,1,1,1,0,1,1,1]
        to_do_nr = 0
        for variable in variable_list:
            if to_do_nr != 5:
                variable.set(1)
            elif to_do_nr != 5:
                variable.set(0)
            to_do_nr = to_do_nr + 1
        progress.resume = 0

    if progress.steps != 0:
        percent = ((progress.steps - sum(progress.to_do)) * 100) / progress.steps
    else:
        percent = 100

    return percent

##Steps mark work as done.
def steps_status_done(step_nr):
    if progress.status[step_nr] == 1:
        return " [done]"
    elif progress.status[step_nr] == 0:
        return ""

##This function will receive status from gromacs2 class and change it to global variable.
def status_update(input_status):
    global status
    status = input_status
    print status[1]

##Help window
def helpWindow(master):
    root = Toplevel(master)
    root.wm_title("Help Window")
    frame = Frame(root)
    frame.pack()

    w = Label(frame, text=help_option())
    w.pack()
    ok_button = Button(frame, text = "OK", command=root.destroy)
    ok_button.pack()

##Log window
def logWindow():
    import sys
    if sys.platform == "linux2":
        cmd = "xdg-open " + project_dir + "log.txt"
        executeSubprocess(cmd)
    elif sys.platform == "darwin":
        cmd = "open " + project_dir + "log.txt"
        executeSubprocess(cmd)
    elif sys.platform.startswith('win'):
        cmd = "start " + project_dir + "log.txt"
        executeSubprocess(cmd)

##Clean message in tkMessageBox
def cleanMessage():
    tkMessageBox.showinfo("Clean", "Temporary files are now removed!\nPlease restart plugin.")
    clean_option()

##This warning message will show if no molecule is selected, but user want to proceed
def no_molecule_warning():
    tkMessageBox.showinfo("No Molecule Selected", "Please choose any molecule before using this option.")

##This function will start real workflow of the plugin, once everything is set
def dynamics():
    print "Starting PyMOL plugin 'dynamics' ver."+plugin_ver+" by Tomasz Makarewicz"
    global status, stop, gromacs, project_name

    file_path = project_dir + project_name
    os.chdir(project_dir)
    stop = 0

    ##Saving configuration files
    if status[0] == "ok" and stop == 0 and progress.to_do[0] == 1:
        mdp_files()
        if status[0] == "ok":
            progress.status[0] = 1
            progress.to_do[0] = 0
            #Pickle trick
            progress.status = progress.status
            progress.to_do = progress.to_do
            save_options()

    ##Counting topology
    if status[0] == "ok" and stop == 0 and progress.to_do[1] == 1 and progress.x2top == 0:
        status = gromacs2.pdb2top(file_path, project_name)
        if status[0] == "ok":
            progress.status[1] = 1
            progress.to_do[1] = 0
            save_options()

    elif  status[0] == "ok" and stop == 0 and progress.to_do[1] == 1 and progress.x2top == 1:
        status = gromacs2.x2top(file_path, project_name)
        if status[0] == "ok":
            progress.status[1] = 1
            progress.to_do[1] = 0
            save_options()

    ##Adding water box
    if status[0] == "ok" and stop == 0 and progress.to_do[2] == 1:
        status = gromacs2.waterbox(file_path, project_name)
        if status[0] == "ok":
            progress.status[2] = 1
            progress.to_do[2] = 0
            save_options()

    ##Adding ions
    if status[0] == "ok" and stop == 0 and progress.to_do[3] == 1:
        status = gromacs2.saltadd(file_path, project_name)
        if status[0] == "ok":
            progress.status[3] = 1
            progress.to_do[3] = 0
            save_options()
    elif status[0] == "ok" and stop == 0 and progress.to_do[3] == 0 and progress.status[3] == 0:
        shutil.copy(project_name+"_solv.gro",project_name+"_b4em.gro")      

    ##EM    
    if status[0] == "ok" and stop == 0 and progress.to_do[4] == 1:
        status = gromacs2.em(file_path, project_name)
        if status[0] == "ok":
            progress.status[4] = 1
            progress.to_do[4] = 0
            save_options()
    elif status[0] == "ok" and stop == 0 and progress.to_do[4] == 0 and progress.status[4] == 0:
        shutil.copy(project_name+"_b4em.gro",project_name+"_b4pr.gro")  

    ##PR
    if status[0] == "ok" and stop == 0 and progress.to_do[5] == 1:
        status = gromacs2.pr(file_path, project_name)
        if status[0] == "ok":
            progress.status[5] = 1
            progress.to_do[5] = 0
            save_options()
    elif status[0] == "ok" and stop == 0 and progress.to_do[5] == 0 and progress.status[5] == 0:
        shutil.copy(project_name+"_b4pr.gro",project_name+"_b4md.gro")

    ##Restraints
    if status[0] == "ok" and stop == 0 and progress.to_do[6] == 1:
        status = gromacs2.restraints(project_name)
        if status[0] == "ok":
            progress.status[6] = 1
            progress.to_do[6] = 0
            save_options()

    ##MD
    if status[0] == "ok" and stop == 0 and progress.to_do[7] == 1:
        status = gromacs2.md(file_path, project_name)
        if status[0] == "ok":
            progress.status[7] = 1
            progress.to_do[7] = 0
            save_options()

    ##Trjconv
    if status[0] == "ok" and stop == 0 and progress.to_do[8] == 1:
        status = gromacs2.trjconv(file_path, project_name)
        show_multipdb()
        progress.status[8] = 1
        progress.to_do[8] = 0
        save_options()

    ##Calculating vectors
    if status[0] == "ok" and stop == 0 and progress.to_do[9] == 1 and prody_true == 1:
        vectors_prody.prody()
        vectors_prody.nmd_format()
        vectors_prody.show_vectors()
        progress.status[9] = 1
        progress.to_do[9] = 0
        save_options()
    elif status[0] == "fail":
        print status[1]
        if stop == 0:
            error_message()

##Saving configuration files
def mdp_files():
    if not os.path.isfile(dynamics_dir + "em.mdp"):
        em_file.save_file()
    if not os.path.isfile(dynamics_dir + "pr.mdp"):
        pr_file.save_file()
    if not os.path.isfile(dynamics_dir + "md.mdp"):
        md_file.save_file()

##Show multimodel PDB file in PyMOOL
def show_multipdb():
    try:
        cmd.hide("everything", project_name) #PyMOL API
    except:
        pass
    cmd.load(project_name+"_multimodel.pdb") #PyMOL API

##Saving tar.bz file
def save_file(destination_path):
    print "Saving"
    import tarfile
    save_options()
    tar = tarfile.open(destination_path+".tar.bz2", "w:bz2")
    tar.add(project_dir, recursive=True, arcname=project_name)
    tar.close()
    os.remove(destination_path)

##Load tar.bz file
def load_file(file_path):
    print "Loading file: " + file_path
    import tarfile
    tar = tarfile.open(file_path, "r:bz2")
    names = tar.getnames()
    #Backup same name folder if file is loaded
    if os.path.isdir(dynamics_dir + names[0]) == True:
        back_folder = dynamics_dir + names[0] + "_back"
        while os.path.isdir(back_folder) == True:
            back_folder = back_folder + "_b"
        os.rename(dynamics_dir + names[0], back_folder)
    tar.extractall(dynamics_dir)
    global project_dir, project_name
    project_name = names[0]
    setGromacsProjectDir()
    load_options()

##Save all settings to options.pickle file
def save_options():
    global vectors_prody
    if prody_true == 0:
        vectors_prody = 0
    print "updating project files"
    if os.path.isdir(project_dir) == False:
        os.makedirs(project_dir)
    destination_option = file(project_dir + "options.pickle", "w")
    pickle_list = [plugin_ver, gromacs.version, gromacs2, em_file, pr_file, md_file, progress, vectors_prody]
    pickle.dump(pickle_list, destination_option)
    del destination_option

##Load all settings from options.pickle file    
def load_options():
    global gromacs2, em_file, pr_file, md_file, progress, vectors_prody

    pickle_file = file(project_dir +"options.pickle")
    options = pickle.load(pickle_file)

    print "Loading project " + project_name
    print "Project was created for Dynamics PyMOL Plugin"+options[0]+" and GROMACS "+options[1]
    if gromacs.version != options[1]:
        print "GROMACS versions is different for loaded file."

    if options[0][1:4] == "2.2":
        gromacs2.update({"force" : options[2].force, "water" : options[2].water, "group" : options[2].group, "box_type"  : options[2].box_type, "hydro" : options[2].hydro,
        "box_distance"  : options[2].box_distance, "box_density" : options[2].box_density, "restraints_nr" : options[2].restraints_nr, "neutrality" : options[2].neutrality,
        "salt_conc" : options[2].salt_conc, "positive_ion" : options[2].positive_ion, "negative_ion" : options[2].negative_ion, "explicit" : options[2].explicit})
        em_file = options[3]
        pr_file = options[4]
        md_file = options[5]
        progress = options[6]
        if prody_true == 1 and options[7] != 0:
            vectors_prody = options[7]
    elif options[0][1:4] == "2.1":
        print "plugin 2.1 compatibility layer"
        gromacs2.update({"force" : options[2].force, "water" : options[2].water, "group" : options[2].group, "box_type"  : options[2].box_type, "hydro" : options[2].hydro,
        "box_distance"  : options[2].box_distance, "box_density" : options[2].box_density, "restraints_nr" : options[2].restraints_nr, "neutrality" : options[2].neutrality,
        "salt_conc" : options[2].salt_conc, "positive_ion" : options[2].positive_ion, "negative_ion" : options[2].negative_ion})
        em_file = options[3]
        pr_file = options[4]
        md_file = options[5]
        progress = options[6]
        gromacs2.update({"explicit" : options[7]})
        if prody_true == 1 and options[8] != 0:
            vectors_prody = options[8]
    else:
        print "Warning. Importing projects from plugin version " + options[0] + " is not supported. Aboring import."

##Text for "Help"
def help_option():
    help_message = """This is the dynamics PyMOL Plugin.
This software (including its Debian packaging) is available to you under the terms of the GPL-3, see "/usr/share/common-lic enses/GPL-3".
Software is created and maintained by Laboratory of Biomolecular Systems Simulation at University of Gdansk.
Contributors:
- Tomasz Makarewicz (btchtm@ug.edu.pl)
- Ajit B. Datta (ajit@jcbose.ac.in)
- Sara Boch Kminikowska
- Manish Sud (msud@san.rr.com; URL: www.MayaChemTools.org)

Full manual is available to you on project website: https://github.com/tomaszmakarewicz/Dynamics/raw/master/manual.odt
or as a file: /usr/share/doc/dynamics-pymol-plugin/manual.odt

The purpose of this plugin is to perform molecular dynamics simulation by GROMACS using easy graphical tool and powerful molecular viewer.

To use this program run it as a PyMOL plugin.
Choose molecule (PDB) for which you want to perform molecular dynamics simulation (left column).
Choose force field and water model options in the middle column.
Choose any additional options in the right column.
Press OK button.
Click Start button and wait till calculation is finished.
Multimodel PDB file will be displayed in PyMOL viewer.
You can click Play button in order to see animation."""
    return help_message

##Clean function
def clean_option():
    shutil.rmtree(dynamics_dir)
    print "Temporary files are now removed."

##If molecular dynamics simulation fails, this function will show the error
def error_message():

    global error

    log = open(project_dir+"log.txt","r")
    log_list = log.readlines()

    error_start_line = 0
    while log_list[error_start_line] != "Fatal error:\n":
        error_start_line = error_start_line + 1
    error_end_line = error_start_line
    while log_list[error_end_line] != "-------------------------------------------------------\n":
        error_end_line = error_end_line + 1
    error_list = log_list[error_start_line:error_end_line]
    error = ""
    for line in error_list:
        error = error + line
    print error

[ghost]

Hi ggothar, Sorry for the late answer, but I am on holidays. Thank you for your interest in the project and code donation. I have edited your post a little bit to make code viewing more clean. I am also attaching diff from your code, which will make it easier to view your changes. At the moment plugin is supporting Microsoft Windows via Cygwin compiled GROMACS: https://pymolwiki.org/index.php/GROMACS_Plugin#Windows.2FCygwin , but using Debian GROMACS directly sounds like interesting option. At the moment I feel that adding proper execution command to "gmxExes" list for WSL GROMACS is better option than modifying every "executeAndMonitorSubprocess" call. I will investigate on this issue further once I am back from the holidays. Again thank you for your input. Best regards, Tomek

Diff:

diff -Naur a/pymol_plugin_dynamics.py b/pymol_plugin_dynamics.py
--- a/pymol_plugin_dynamics.py  2017-06-27 13:14:09.716275000 +0200
+++ b/pymol_plugin_dynamics.py  2017-06-27 17:50:08.754529824 +0200
@@ -1,7 +1,7 @@
 #!/usr/bin/env python2
 #-*- coding: utf-8 -*-

-##This software (including its Debian packaging) is available to you under the terms of the GPL-3, see "/usr/share/common-licenses/GPL-3".
+##This software (including its Debian packaging) is available to you under the terms of the GPL-3, see "/usr/share/common-lic enses/GPL-3".
 ##Software is created and maintained by Laboratory of Biomolecular Systems Simulation at University of Gdansk.
 ##Contributors:
 ##- Tomasz Makarewicz (btchtm@ug.edu.pl)
@@ -22,6 +22,9 @@
 import tkSimpleDialog, tkMessageBox, tkFileDialog, Pmw
 ##Import libraries from PyMOL specific work.
 from pymol import cmd, stored, cgo
+from os.path import expanduser
+
+

 ##Check for ProDy
 try:
@@ -54,7 +57,7 @@
        self.version =  gmxVersion
        self.command =  gmxExe

-       # Track current directiry and switch to dynamics_dir before invoking gmx...
+       # Track current directory and switch to dynamics_dir before invoking gmx...
        current_dir = os.getcwd()
        os.chdir(dynamics_dir)

@@ -152,7 +155,7 @@

        gmxStdoutFilePath = "test_gromacs.txt"

-       cmd = self.command + " pdb2gmx -f  test_gromacs.pdb -o test_gromacs.gro -p test_gromacs.top"
+       cmd =self.command + " pdb2gmx -f  test_gromacs.pdb -o test_gromacs.gro -p test_gromacs.top"
        executeSubprocess(cmd,  gmxStdinFilePath, gmxStdoutFilePath)

        lista_gromacs = readTextLines(gmxStdoutFilePath)
@@ -190,7 +193,7 @@
        fo.write( "q")
        fo.close()

-       cmd = self.command+" make_ndx -f "+project_name+".pdb -o index.ndx" 
+       cmd = self.command+" make_ndx -f "+project_name+".pdb -o index.ndx"
        executeSubprocess(cmd,  "gromacs_stdin.txt", "restraints.log")

        index_list = readTextLines("restraints.log")
@@ -284,7 +287,7 @@
        fo.close()

        command = gromacs.command +" pdb2gmx -f " + project_name + ".pdb -o " + project_name + ".gro -p " + project_name + ".top " + hh
-       executeAndMonitorSubprocess(command,  'gromacs_stdin.txt', 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+".gro") == True:
            status = ["ok", ""]
@@ -293,7 +296,7 @@
            status_update(status)

            command = gromacs.command+" pdb2gmx -ignh -f "+project_name+".pdb -o "+project_name+".gro -p "+project_name+".top "+hh
-           executeAndMonitorSubprocess(command,  'gromacs_stdin.txt', 'log1.txt', 'log.txt')
+           executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+".gro") == True and stop == 0:
            status = ["ok", "Calculated topology using Force fields"]
@@ -312,7 +315,7 @@
            pass

        command = gromacs.command+" x2top -f "+project_name+".pdb -o "+project_name+".top"
-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+".top") == True and stop == 0:
            status = ["ok", "Calculating structure using trjconv."]
@@ -326,7 +329,7 @@
            fo.close()

            command = gromacs.command+" trjconv -f "+project_name+".pdb -s "+project_name+".pdb -o "+project_name+".gro"
-           executeAndMonitorSubprocess(command,  'gromacs_stdin.txt', 'log1.txt', 'log.txt')
+           executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

            if os.path.isfile(file_path+".gro") == True and stop == 0:
                status = ["ok", "Calculated structure using trjconv."]
@@ -349,7 +352,7 @@

        status_update(status)
        command = gromacs.command+" editconf -f "+project_name+".gro -o "+project_name+"1.gro -c "+box_type+distance+density
-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        water_name = gromacs.water_list[self.water-1][1][4:8].lower()
        print water_name
@@ -365,7 +368,7 @@
        status = ["ok", "Adding Water Box"]
        status_update(status)

-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"1.gro") == True and stop == 0:
            status = ["ok", "Water Box Added"]
@@ -388,7 +391,7 @@

        command = gromacs.command+" grompp -f em -c "+project_name+"_solv.gro -o "+project_name+"_ions.tpr -p "+project_name+".top"
        status_update(status)
-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        fo = open("gromacs_stdin.txt", "w")
        fo.write( "13")
@@ -398,7 +401,7 @@
        status_update(status)

        command = gromacs.command+" genion -s "+project_name+"_ions.tpr -o "+project_name+"_b4em.gro "+positive+negative+salt+neu+" -p "+project_name+".top"
-       executeAndMonitorSubprocess(command,  'gromacs_stdin.txt', 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_b4em.gro") == True and stop == 0:
            status = ["ok", "Ions added successfully"]
@@ -425,10 +428,10 @@

        status_update(status)       
        command = gromacs.command+" grompp -f em -c "+project_name+"_b4em -p "+project_name+" -o "+project_name+"_em"
-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        command = gromacs.command+" mdrun -nice 4 -s "+project_name+"_em -o "+project_name+"_em -c "+project_name+"_b4pr -v"
-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_em.tpr") == True and stop == 0:
            status = ["ok", "Energy Minimized"]
@@ -449,10 +452,10 @@

        status_update(status)
        command = gromacs.command+" grompp -f pr -c "+project_name+"_b4pr -r "+project_name+"_b4pr -p "+project_name+" -o "+project_name+"_pr"
-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        command = gromacs.command+" mdrun -nice 4 -s "+project_name+"_pr -o "+project_name+"_pr -c "+project_name+"_b4md -v"
-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_pr.tpr") == True and stop == 0:
            status = ["ok", "Position Restrained MD finished"]
@@ -475,7 +478,7 @@

        status_update(status)
        command = gromacs.command+" genrestr -f "+project_name+".pdb -o posre_2.itp -n index_dynamics.ndx"
-       executeAndMonitorSubprocess(command,  'gromacs_stdin.txt', 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile("posre_2.itp") == True and stop == 0:
            status = ["ok", "Added Restraints"]
@@ -507,10 +510,10 @@

        status_update(status)
        command = gromacs.command+" grompp -f md -c "+project_name+"_b4md  -p "+project_name+" -o "+project_name+"_md"
-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        command = gromacs.command+" mdrun -nice 4 -s "+project_name+"_md -o "+project_name+"_md -c "+project_name+"_after_md -v"
-       executeAndMonitorSubprocess(command,  None, 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  None, 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_md.tpr") == True and stop == 0:
            status = ["ok", "Molecular Dynamics Simulation finished"]
@@ -535,7 +538,7 @@

        status_update(status)
        command = gromacs.command+" trjconv -f "+project_name+"_md.trr -s "+project_name+"_md.tpr -o "+project_name+"_multimodel.pdb"
-       executeAndMonitorSubprocess(command,  'gromacs_stdin.txt', 'log1.txt', 'log.txt')
+       executeAndMonitorSubprocess("bash -lic '" + command + "'",  'gromacs_stdin.txt', 'log1.txt', 'log.txt')

        if os.path.isfile(file_path+"_multimodel.pdb") == True and stop == 0:
            status = ["ok", "Finished!"]
@@ -910,7 +913,7 @@

    project_name = "nothing"

-   homeDir = os.getenv("HOME")
+   homeDir = expanduser("~")

    gmxHomeDirPath = os.path.abspath(homeDir)
    dynamics_dir = os.path.join(gmxHomeDirPath, '.dynamics', '')
@@ -937,7 +940,7 @@

    print "Running command: " + command + "; STDIN: " + stdinMsg + "; STDOUT: " + stdoutMsg

-   returnCode = subprocess.call(command, stdin=stdinFile, stdout=stdoutFile, stderr=subprocess.STDOUT, shell=True)
+   returnCode = subprocess.call("bash -lic '" + command + " '", stdin=stdinFile, stdout=stdoutFile, stderr=subprocess.STDOUT, shell=True)

    if stdinFilePath:
        stdinFile.close()
@@ -972,7 +975,7 @@

    print "Running command: " + command + "; STDIN: " + stdinMsg + "; STDOUT: " + stdoutMsg

-   gmx = subprocess.Popen(command,  stdin=stdinFile, stdout=stdoutFile, stderr=subprocess.STDOUT, shell=True)
+   gmx = subprocess.Popen("bash -lic '" + command + " '",  stdin=stdinFile, stdout=stdoutFile, stderr=subprocess.STDOUT, shell=True)
    while gmx.poll() is None:
        if stop == 1:
            gmx.kill()
@@ -1042,7 +1045,7 @@
    error = ""

    # Make sure HOME environment variable is defined before setting up directories...
-   homeDir = os.getenv("HOME") 
+   homeDir = expanduser("~")
    if homeDir:
        os.chdir(homeDir)
    else:
@@ -2857,7 +2860,7 @@
 ##Text for "Help"
 def help_option():
    help_message = """This is the dynamics PyMOL Plugin.
-This software (including its Debian packaging) is available to you under the terms of the GPL-3, see "/usr/share/common-licenses/GPL-3".
+This software (including its Debian packaging) is available to you under the terms of the GPL-3, see "/usr/share/common-lic enses/GPL-3".
 Software is created and maintained by Laboratory of Biomolecular Systems Simulation at University of Gdansk.
 Contributors:
 - Tomasz Makarewicz (btchtm@ug.edu.pl)