[gmx-users] Solvating in a solvent other than water

[Justin Lemkul]

On 9/19/15 10:07 AM, Pallavi Banerjee wrote:
> Hello Users,
>
> I have a system of three polymer chains (30 monomers), all of which I
> insert into a polymer matrix (5 monomers). I have an equilibrated box of
> the matrix that would act as the solvent in my case. Since this non-aqueous
> solvent box is too small, I expand it using genconf. But, on energy
> minimizing this box, it forms blocks within the box, which precludes me
> from equilibrating it. How do you circumvent this?
>

What does "blocks within the box" mean?  Can you provide an image?  Have you 
tried equilibrating it and it fails, or you just assume that you'll have a problem?

-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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