On 5/12/13 12:54 PM, Hyunjin Kim wrote:
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?
Thanks a lot. I chose residues 1 and 25.
I understood that from the original post. What I was asking about was the exact
groups you chose from the g_energy selection menu.
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
wrong?
You will only get decomposed terms in the context of the interactions of those
residues. Again, seeing the full g_energy selection menu would help us in
solving your problem. Thus far, I can see no evidence that Gromacs has done
anything wrong, but I also haven't seen any diagnostic evidence of what you have
tried to do. Please provide the details I have requested.
-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
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