[gmx-users] Potential for Frozen atoms

[Justin Lemkul]

On 4/16/14, 12:07 AM, sukriti002 wrote:
> Hi,
>
> I wanted to find out site-site potential between two Copper(Cu+2) ions at a
> particular distance and fixed geometry. So I constructed a box containing 2
> Cu+2 and 2 sulfate ions very far away to make the system charge zero. Then i
> froze these atoms and did energy minimization step. But in result I get zero
> potential energy. Can anyone please let me know what went wrong? I can i
> find out this potential at a particular ion-ion distance?
>

Please post the full .mdp file (copied and pasted into the email, not attached) 
and details of exactly how large the box is and how far apart the Cu ions are.

-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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