[gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints

[Justin Lemkul]

On 2/9/15 5:07 AM, Antara mazumdar wrote:
> Hi,
> I minimised a heterogenous lipid system of 1464  DOPC and DOPG and applied
> position restraints as well as had vdwradii.dat file for genbox step. Yet
> after minimisation, there are gaps between the lipid molecules. Pls suggest
> a remedy.
>

Equilibrate thoroughly.

-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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