[gmx-users] about tutorial on virtual sites

[Justin Lemkul]

On 4/19/14, 11:06 AM, sujithkakkat . wrote:
> Hello Justin,
>
>    I found that in  the virtual sites section of your tutorial, the energy
> values of the system large positive . You had warned in the topology file
> that the choice of the partial charges used are not guaranteed to work
> always with OPLSAA . However, the momentum of inertial values points
> indicate proper dynamics of the system.
>
> Is the positive potential energy an out come of using the OPLSAA forcefield
> ? Is it normal to have positive potential energy?
>

Yes, that is normal.  Most gas-phase simulations will have a positive energy.

-Justin

-- 
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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

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