[gmx-users] Positive energy .

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================