[gmx-users] decomposing the energy

Justin A. Lemkul jalemkul at vt.edu
Sat May 14 13:11:52 CEST 2011

Ramachandran G wrote:
> Hello gmx users:
>       I did 1ns simulation for my system and have the trajectory and 
> energy files.
> Now i want to see the energy of some specific residues. So, i 
> decompose(separated) the energy groups and edited the mdp file.
> Using the mdp file, i created a new tpr file and rerun the mdrun using 
> the trajectory file. But when i compared the total energy between the 
> old and new one, it differs a lot.
> I am doing some mistakes somewhere. Can anyone help me please. Thanks.

Maybe, maybe not.  Without seeing the .mdp settings and the data that you're 
looking at, all anyone can do is guess.  You also haven't stated what type of 
trajectory (i.e. .xtc or .trr) you're using as -rerun input.  If you're using an 
.xtc file, there is no velocity information, so any property related to 
velocities (most notably kinetic energy, but several others as well) will be 
zero.  I suspect this is probably where the discrepancy is, but it is not a 
problem.  Using energygrps is only useful for decomposing short-range nonbonded 
energy terms, nothing else.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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