I am a beginner and I found some tutorials on GROMACS website. Although I was able to follow some of steps through typing commands in ssh window, but I wasn't successful to run energy minimization step because I don't know how to write the script file specifying number of processors that can be utilized for running energy minimization. your help is really much appreciated.
The MDP file for energy minimization can be found here: http://www.mdtutorials.com/gmx/lysozyme/Files/minim.mdp
To generate TPR file for energy minimization:
gmx grompp -f minim.mdp -c filename.gro -p topol.top -o TPR-filename.tpr
Typically, you can run energy minimization on a local computer/ laptop unless it's a huge system you're dealing with. For running a gromacs command on a supercomputer, mpirun is used. This is not shown on the mdtutorials webpage. You have to setup a bash script (.sh extension) containing multiple job options, then load the gromacs module, and finally enter the mpirun command like the following:
mpirun -np 48 mdrun_mpi -v -s TPR-filename.tpr -deffnm filename
Here, "-np" indicates number of processors. If you're using gromacs version above 2016, you may have to replace "mdrun_mpi" with "gmx_mpi mdrun". Enquire with your supercomputer's IT team/website to refer to an example job submission script, and how to submit it.
Here I hope you find this link helpful:
http://www.mdtutorials.com/gmx/free_energy/04_EM.html
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