[gmx-users] Polymer not diffusing into membrane

[Alex s]

I obtained all of my forcefield, coordinate and topology files from the MARTINI website.

> Date: Wed, 13 Aug 2014 11:29:52 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Polymer not diffusing into membrane
> 
> 
> 
> 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
> 
> -- 
> ==================================================
> 
> 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
> http://mackerell.umaryland.edu/~jalemkul
> 
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