<DIV >
<DIV>Thank you, Mark</DIV>
<DIV>I modify the .mdp file as follows:</DIV>
<DIV>energygrps = Protein sol Cl --> energygrps = res57_62 res102_109</DIV>
<DIV> </DIV>
<DIV>and make tpr file:</DIV>
<DIV>grompp -f md.mdp -c pr_out.gro -p topol.top -o rerun.tpr -n index.ndx</DIV>
<DIV>mdrun -rerun test.xtc -s rerun.tpr</DIV>
<DIV>It gives warings:</DIV>
<DIV>WARNING: Some frames do not contain velocities.<BR> Ekin, temperature and pressure are incorrect,<BR> the virial will be incorrect when constraints are present.<BR>I found files traj.trr and ener.edr; </DIV>
<DIV> </DIV>
<DIV>However, I am not certain whether I did right? Is any extra constraints needed?</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #a0c6e5 2px solid; MARGIN-RIGHT: 0px">
<HR color=#a0c6e5 SIZE=1>
From: "Mark Abraham" <MARK.ABRAHAM@ANU.EDU.AU><BR>Sent :2006-09-22 11:41:07<BR>To:"Discussion list for GROMACS users" <GMX-USERS@GROMACS.ORG><BR>Title: Re: [gmx-users] calculate the interaction energy between different parts of protein<BR><BR><BR><PRE style="WIDTH: 100%; WORD-WRAP: break-word">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.
Mark
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