Hi, Won
Ok, what I did was not exactly as is described.
I attach the bash script that I made to do this
I use the trajectory file to extract EACH frame and safe it in an independent
file using trjconv . And when I do the extraction, I only extract the protein
of interest, this can be done because you should provide an index.ndx file.
Once I have these files (usually thousands), I run a short MD sim for each one
(1fs is the MD time). because this simulation is in vacuum you will get the
potential energy for that structure. From the edr file generated in this
simulation I extracted the potential energy using g_energy.
Usually I took the second instant, not the first one, because it is more
accurate (the last line of the script does this.)
John Michael
----------------
#!/bin/bash
#Location of the gromacs files
trjconv -f protein.NVE.xtc -sep -o LFG..gro -n index.ndx -s protein.NVEs.tpr
for i in `seq 0 2000`; do
echo "================================"
echo ENERGY CALCULATION $i
echo "====== Simulation ============="
grompp_d_mpi -v -f md-nves.mdp -c LFG.$i.gro -p T1-1-PRout2.top -o pro.e.$i.tpr
-po mdout.$i.mdp -maxwarn 4
mdrun_d_mpi -e pro.e.$i.edr -deffnm pro.e.$i
done
for i in `seq 0 2000`; do
g_energy_d_mpi -f pro.e.$i.edr -o ener.$i < pot.txt
done
#after obtain this file, it is necessary to sort it and clean the first colunm
grep 0.001000 *.xvg > ener1.enr
----------------------------------------------------------------------------------------
Date: Fri, 5 Jul 2013 06:26:35 -0700
From: ml-node+s5086n5009597...@n6.nabble.com
To: cyberj...@hotmail.com
Subject: Re: About Potential energy calculation
Hi, nice to read this post. I need to do the same thing as you, but I
am very new in Gromacs, can you show me how to seperate the protein part and
generate the neceesary file to do "mdrun -rerun"?
Thanks in advance
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