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HITS-MCM / gromacs-ramd

Random Acceleration Molecular Dynamics in GROMACS
GNU Lesser General Public License v2.1
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no content in out file #44

Open haoxuanluo731 opened 4 months ago

haoxuanluo731 commented 4 months ago

hello,I run the Submit_15_jobs_gromacs-ramd.sh，I have fininsh the project and get 15 trj，but in every files，there is nothing in out file,so I cant run the grep "GROMACS will be stopped after" TRJ/out > times_1.dat,to get content.can you give me a solvlution 屏幕截图 2024-07-23 154818

BerndDoser commented 4 months ago

Thank you for reporting. The script you are calling is part of a downstream process described in the tutorial:

https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-gromacs/

I'm not directly involved in this tutorial, but I can figure out what is going wrong. For this, I need more information.

haoxuanluo731 commented 4 months ago

thank you for your reply

md.log this is gromacs-ramd version 屏幕截图 2024-07-23 204815 this is version of tutorial tar files 屏幕截图 2024-07-23 204927

BerndDoser commented 4 months ago

I've noticed that the md.log file appears to be in good shape, and it contains the necessary information about "GROMACS will be stopped after". It seems to me that the command mentioned in the tutorial:

grep "GROMACS will be stopped after" TRJ*/*out > times_1.dat

should be:

grep "GROMACS will be stopped after" TRJ*/md.log > times_1.dat

I will escalate this issue to the group for further review.

haoxuanluo731 commented 4 months ago

thank you for your reply,if this further view have new information,can you ask the details for me

haoxuanluo731 commented 4 months ago

i also have a question,when i use tauRAMD.py,what python package should i install

BerndDoser commented 4 months ago

The Python dependencies of the tutorial are listed under Required Software and Data.

Python 3.x (libraries: numpy.py; matplotlib, pylab, seaborn, scipy, ParmEd)
haoxuanluo731 commented 4 months ago

thank you for your reply

haoxuanluo731 commented 4 months ago

I want ask a question,when i want to use MD-IFP to analysis trajectory produced from Gromacs and produced IFP datadbase,what files should I use,in your example I only find the .py for NAMD and the example for NAMD,don not find Trajectories.py and IFP generation.py for Gromacs

StefanGIT commented 4 months ago

I want ask a question,when i want to use MD-IFP to analysis trajectory produced from Gromacs and produced IFP datadbase,what files should I use,in your example I only find the .py for NAMD and the example for NAMD,don not find Trajectories.py and IFP generation.py for Gromacs

Are you refering to the MD-IFP analysis described here: https://github.com/HITS-MCM/MD-IFP