[gmx-users] Energy-groups?

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> Hello,
> 
>    I want to plot the interaction potential energy between my solute and 
> solvent. In my .mdp file I did not mention anything under energygrps,so 
> I am thinking it calculates the energies for the whole system. But is 
> there a way I can extract say for example LJ-14 term between my solute 
> and solvent using the same .edr file? Or would I have to specify my 
> energygrps and run the simulation again.
> 

1-4 interactions are intramolecular, so there should be no solute-solvent 1-4 
term.  If you want nonbonded potentials decomposed, yes, you have to rerun your 
trajectory (mdrun -rerun, not from scratch) with a .tpr file specifying the 
desired groups.

-Justin

> Thanks.
> 
> Nisha
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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