pythonic_martini

Python scripts for creating and simulating macromolecules using MARTINI / GROMACS, targeted for peptide amphiphiles.

Built using python3.8

Software prerequisites:

• Python3 (Tested on version 3.8)
• Python2 (for martinize.py)
• numpy (Tested on version 1.17.4)
• scipy
• vmd (Tested on version 1.9.4a43)
• GROMACS (Tested on version 2020.2)

(vmd and gromacs should be callable at the command line. Look at the Installation tips for solutions to problems faced by people during installation)

You can download the package and run the example script using the following commands. Running example_script will create the directory 'example', then prepare and run the PA-peptide coassembly simulation inside it.

git clone https://github.com/stupplab/pythonic_martini.git
cd pythonic_martini
python example_script.py

If you want to run the example script from anywhere, i.e., import pythonic_martini from anywhere, install the package in you local python package directory by running

python setup.py install --user

Another installation method

python setup.py sdist
pip install dist/pythonic_martini-0.1.tar.gz

Typical simulation steps when using MARTINI to simulation a peptide amphiphile molecule are:

• Make all-atom .pdb file (here using vmd) from a starting pdb file containing generic structure for the molecule
• Prepare coarge-grained files (itp, top, pdb) using martinize.py that uses the all-atom file.
• Create the simulation box using gromacs filled with coarse-grained molecules
• Solvate the box
• Add ions as needed
• Run minimization (tiny simulation) to relax the initialization artifacts
• Run equilibration (main simulation)

main.py is the main script that lets you do all the above as shown by the example

Additional details

variable ending with 'filename' are file names with extensions, whereas variables ending with 'name' are without extensions and will be used to read/write from multiple extensions.

Original or selectively modified martini files are:\

• martini_v2.0_ions.itp
• martini_v2.2.itp
• martinize.py
• top_all36_prot_forPAs.rtf

Development - Adding new code

Any changes/additions you make to the code, do it in a new branch. To see which branch you are on, type

$ git branch

Create a new branch

$ git branch branchname

Go into that branch

$ git checkout branchname

Now this is your branch and you can do any modififications and additions to code. These changes are still in your local workstation. You need to add these to Github repository using git. Let's say you added file1 and modified file file2.py. Then do,

$ git add file1 file2
$ git commit -m "Message telling what these changes are for."
$ git push origin branchname

The last command pushes the code to the branch branchname in the origin, which is already set to be the Github address of the this repository pythonic_martini. branchname is created if it doesn't already exists. You can run $ git diff to check if there a difference between the files of this branch in your workstation and the Github server.

You can make as make changes as you want using this process but these changes are still in the branch you created and not in the primary branch of this repository called master. You can keep using this modified version of the code for your personal use. When and if you think these changes should be incorporated in the master branch, create a Pull request. For this, go to the Github page of your branch and click Pull request. Fill up the details asked and submit. On the first time, command git push origin branchname also generates a link that you can just copy on your browser to access the pull request page. It may look something like https://github.com/stupplab/pythonic_martini/pull/new/branchname.

The maintainer of the repository will now look at the pull request, resolve any conflicts and merge the code as required.

Installation tips

VMD - for MacOS/LINUX

Part of pythonic_script that runs vmd, assumes that vmd is callable from the command line. Now vmd is callable from command line when VMD package is installed from the source in the system PATH. However, people usually install VMD as an app in the Applications directory. Follow the instructions below to create a callable vmd link.

Go to the directory of your VMD app's startup.command, which is the actual executable that runs the VMD. If your app's name is VMD 1.9.4a43-Catalina-Rev6, then the executable path should look like /Applications/VMD 1.9.4a43-Catalina-Rev6.app/Contents/MacOS/startup.command

cd /Applications/VMD\ 1.9.4a43-Catalina-Rev6.app/Contents/MacOS

Create a symbolic vmd link

ln -s startup.command vmd

Add Applications/VMD\ 1.9.4a43-Catalina-Rev6.app/Contents/MacOS to PATH in the configuration file of your shell. For example, for bash shell, open .bash_profile in the home directory. Add the line export PATH="Applications/VMD\ 1.9.4a43-Catalina-Rev6.app/Contents/MacOS:$PATH.

This should make your vmd callable from the command line. (Remember to open a new terminal window to start calling vmd)