[gmx-users] Script for looping n simulations

[Neena Susan Eappen]

Hi Justin,

I tried that script out, but I want the output in a different way. So I have n log files (.log), and I want to extract potential energy value say from line x from all n log files. Is there a way I can export all these potential energy values into one text file with one script?

Many thanks,
Neena
________________________________
From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
Sent: Saturday, February 22, 2020 4:28 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Script for looping n simulations

Thank you Miro, but I don't think I found what I wanted in your script. Let me be more clear: I ran n simulations in a loop, I have corresponding n energy files (.edr). I want to extract potential energy from each file. How would I go about that with a script?

Many thanks,
Neena
________________________________
From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
Sent: Saturday, February 22, 2020 2:41 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Script for looping n simulations

Thank you Justin, just sharing the sample script here:
--------------------
#!/bin/bash
for i in {1..n}
do j=$((i+1))
gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr
gmx mdrun -deffnm nvt${j}
gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o md${j}.tpr
gmx mdrun -deffnm md${j}
done
----------------------
Question: Now that I have n .edr files, is there a script I can write to extract say potential energy from these n files?

Thank you for your time and knowledge,
Neena


________________________________
From: Neena Susan Eappen
Sent: Saturday, February 15, 2020 4:44 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Script for looping n simulations

Hello gromacs users,

I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle.

Many thanks,
Neena