[gmx-users] question about energygrps
jalemkul at vt.edu
Sun May 12 19:00:54 CEST 2013
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
>> 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.
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
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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