I see. It did work . Thanks a lot Justin!
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
nishap.pa...@utoronto.ca wrote:
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
Thanks Justin! I do want the non-bonded potential between my solute
and solvent. So in my .mdp file I put my solute and solvent as
energygrps and ran mdrun using this command:
mdrun -s md1.tpr(including energygrps) -rerun md.xtc (my trajectory)
Is that correct? I don't understand how it would be faster or any
different from running the simulation from scratch, because in my
.mdp file it still has time of 100ns. I just modified the energygrps.
It should be significantly faster. In this case, mdrun is not doing
the integration, it's simply using the known positions to re-calculate
energies.
-Justin
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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========================================
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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