[gmx-users] question about energygrps

Hyunjin Kim hyunjink at andrew.cmu.edu
Sun May 12 08:25:09 CEST 2013


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.
In log file, "energygrp-flags[  0]: 0".
I think this means it calculate system energies instead of two specific
groups I choose.

Could you give me advice how to fix this problem?

Thanks in advance.


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