[gmx-users] question about energygrps

Justin Lemkul jalemkul at vt.edu
Sun May 12 14:29:57 CEST 2013

On 5/12/13 2:25 AM, Hyunjin Kim wrote:
> Dear,
> 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, then
> values of all energy terms are same, although I choose different groups.

Which specific groups did you choose?

> 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.



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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