[gmx-users] question about energygrps
hyunjink at andrew.cmu.edu
Sun May 12 18:54:36 CEST 2013
> On 5/12/13 2:25 AM, Hyunjin Kim wrote:
>> I want to calculate LJ and Electrostatic energies between two groups
>> defined in index.ndx during rerun with original trajectory.
>> The following is what I tried:
>> 1. insert "energygrps r_1 r_25" in the test.mdp file.
>> 2. grompp -f test.mdp -c x.gro -o x.tpr -p x.top -n index.ndx
>> 3. mdrun -nt 2 -rerun o.trr -s x.tpr -o x.trr -c x.gro -g x.log -e x.ene
>> The simulation runs properly, but if I collect energy using g_energy,
>> values of all energy terms are same, although I choose different groups.
> Which specific groups did you choose?
Thanks a lot. I chose residues 1 and 25.
>> In log file, "energygrp-flags[ 0]: 0".
>> I think this means it calculate system energies instead of two specific
>> groups I choose.
> Some energy terms are decomposable, most are not. There will be obvious
> differences in group names in the g_energy output.
I thought nonbonded energy terms were supposed to be decomposable, since
the two groups I selected are from one in solute and one in solvent. Am I
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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