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

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to