[gmx-users] calculate the interac tion energy between different parts of pr otein

M. Yan yanmaocai at 126.com
Fri Sep 22 08:59:22 CEST 2006

Thank you, Mark
I modify the .mdp file as follows:
energygrps = Protein sol Cl  --> energygrps = res57_62 res102_109
and make tpr file:
grompp -f md.mdp -c pr_out.gro -p topol.top -o rerun.tpr -n index.ndx
mdrun -rerun test.xtc -s rerun.tpr
It gives warings:
WARNING: Some frames do not contain velocities.
         Ekin, temperature and pressure are incorrect,
         the virial will be incorrect when constraints are present.
I found files traj.trr and ener.edr; 
However, I am not certain whether I did right? Is any extra constraints needed?

From: "Mark Abraham" 
Sent :2006-09-22 11:41:07
To:"Discussion list for GROMACS users" 
Title: Re: [gmx-users] calculate the interaction energy between different parts of protein

M. Yan wrote:
> Hi dear friends,
> I want to analyze the interaction energy between two parts of protein, 
> for instance, residue 57-62 and residue 104-109. g_energy does not work 
> because the file ener.edr did not record this items. How to calculate 
> it from the trajectory file?

Define appropriate energy groups, then use mdrun -rerun.

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