no content in out file

[haoxuanluo731]

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

[BerndDoser]

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.

• Installed version of GROAMCS-RAMD
• Version of the tutorial tar files
• Output of md.log

[haoxuanluo731]

thank you for your reply

md.log this is gromacs-ramd version this is version of tutorial tar files

[BerndDoser]

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]

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

[haoxuanluo731]

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

[BerndDoser]

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]

thank you for your reply

[haoxuanluo731]

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]

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