[gmx-users] Solvating in a solvent other than water
Vitaly V. Chaban
vvchaban at gmail.com
Sat Sep 19 22:32:27 CEST 2015
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
>> 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 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
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users