[gmx-users] Re: Positive Potential Energy after equilibration

[Justin A. Lemkul]

On 6/12/12 8:26 AM, Satish Kamath wrote:
> Dear Sir,
>
> Thank you for your reply. I just ran NPT and the potential stabilizes at
> around +9000. The charge distribution change has reduced a lot of potential
> but it is still positive. My NPT ran for 1ns.
>

Then either the topology is still not suitable or the simulation is not long 
enough.  Make sure you're analyzing other observables to judge the quality of 
your model (RDF, H-bonding, density, etc).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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