[gmx-users] How to calculate energy after production MD

Justin Lemkul jalemkul at vt.edu
Mon Jan 5 13:48:20 CET 2015

On 1/4/15 6:57 PM, Mark Abraham wrote:
> Hi,
> You need to define an index group, use it in a new .mdp file as an energy
> group, and then follow
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

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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