[gmx-users] question about energygrps

[Justin Lemkul]

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

-- 
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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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