[gmx-users] Positive energy .
jalemkul at vt.edu
Tue May 13 18:29:15 CEST 2014
On 5/13/14, 11:21 AM, Rasoul Nasiri wrote:
> Why do you think positive values are doubtful?
> What matters are energy differences between different snapshots
> The absolute energy is meaningless in the FF framework.
Not entirely true. While the actual value itself is totally force
field-dependent and is not a free energy, the fact that the OP is getting
positive energies in the condensed phase is strange. It means that the system
is net-repulsive, which should not be the case, especially if it is solvated in
water, in which hydrogen bonding should dominate.
Without more details about system size, .mdp settings, and force field details,
it's hard to provide the OP with any real suggestions.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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