Two things you have to be careful about:
1- use trr trajectory files. xtc precision is not sufficient and it
will give a lot of discrepancies at least for the bonded terms.
2- set the nstlist to 1 as the neiboring list should be undated for
each frame and not every 5/10 as it is normally set in a regular mdp
file.
On May 14, 2011, at 1:11 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.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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