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 <[email protected]> Sent: Saturday, February 22, 2020 2:41 PM To: [email protected] <[email protected]> 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: [email protected] <[email protected]> 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
