nishap.pa...@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
--
========================================
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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