[gmx-users] Polymer not diffusing into membrane

Justin Lemkul jalemkul at vt.edu
Wed Aug 13 17:30:04 CEST 2014

On 8/13/14, 10:45 AM, Alex s wrote:
> I should've mentioned that the those snapshots are of different system set
> ups. The first snapshot is for a system I set up by doubling the size of
> lipid box and placing the polymer just above the membrane. The second

A little context next time, please.

> snaphshot is for a another system where I left the lipid box size as it was
> after equilibration and placing the polymer above the membrane. The only
> strange thing that I notice is the polymer is being almost 'repelled' by the

That sounds like a force field problem.  What is the source of your parameters?

> bilayer. Also is there an easy way to automatically fill the empty spaces in
> the box with water? The way I do it is quite tedious where I have to manually
> edit water boxes and position them to fill the empty space in the system

That's what genbox (gmx solvate in 5.0) is for.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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