On 12/27/13, 6:00 PM, Ali Alizadeh wrote:
Dear All users,

I have a question about calculation of potential energy for an especial
group. I know I had to

define an energy group in .mdp file. I forgot to do it. I want to know can
I extract this potential

energy by post processing or not? If not this means I must perform my
simulation again?

There is no .mdp option to calculate the potential energy of just a single group. One can excluded nonbonded interactions between pairs of groups or decompose nonbonded energy between pairs of groups.

One could obtain "the potential energy of a group" by stripping out the coordinates of interest from the original trajectory (with trjconv), making a matching .tpr file (with tpbconv), then recalculating energies with mdrun -rerun. Such a quantity would be useless, though.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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