On 14/05/2011 9:11 PM, Justin A. Lemkul wrote:
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.
Strictly speaking, one can decompose bonded energy terms too, with a
well-constructed topology, but I agree with the rest of what Justin said.
Mark
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