[gmx-users] How to calculate energy after production MD
jalemkul at vt.edu
Mon Jan 5 13:48:20 CET 2015
On 1/4/15 6:57 PM, Mark Abraham wrote:
> You need to define an index group, use it in a new .mdp file as an energy
> group, and then follow
But this will only give short-range nonbonded energies. To get the "energy of
the helix" would require extracting the helix from the original .tpr and
trajectory, then mdrun -rerun on this subset of atoms. Of course, that quantity
doesn't actually mean anything...
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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