[gmx-users] RE: About Potential energy calculation

cyberjhon cyberjhon at hotmail.com
Mon Jul 8 22:27:41 CEST 2013

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



#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 "====== 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


for i in `seq 0 2000`; do

g_energy_d_mpi -f pro.e.$i.edr -o ener.$i < pot.txt


#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+s5086n5009597h39 at n6.nabble.com
To: cyberjhon at 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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