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

[Vitaly V. Chaban]

Thermodynamic equilibrium is concluded from the evolution of thermodynamic
quantities, not presence or absence of "blocks within the box".







On Sat, Sep 19, 2015 at 11:19 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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