[gmx-users] free energy binding

[Justin Lemkul]

On 6/4/15 8:41 AM, Daniele Veclani wrote:
> Dear A. Lemkul
>
> I'm writing about the problem with the calculation of  free energy binding.
>
> I used 20 steps for the calculation of the free energy, only three of these
> steps (7,12,19) I find this error. And in these steps simulation terminates
> prematurely.
>

You probably just need better minimization and/or more equilibration in those 
windows, or maybe a shorter time step.

-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 629
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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