[gmx-users] Polymer not diffusing into membrane
as1783 at hotmail.com
Tue Aug 12 19:35:41 CEST 2014
I've run it for 200 ns which I think is long enough allow the polymer to diffuse.
> Date: Tue, 12 Aug 2014 10:41:52 +0200
> From: devicerandom at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Polymer not diffusing into membrane
> How long is your simulation? Are you sure it is long enough to see what you
> want to see?
> On 12 Aug 2014 07:15, "Alex s" <as1783 at hotmail.com> wrote:
> > Dear Gromacs users
> > I'm not sure if this a question suitable for this forum but I would
> > greatly appreciate it if you can help me in anyway regarding this issue.
> > I've have a system made up of a lipid bilayer, water and a single chain
> > polymer. My aim is to place the polymer just above the lipid bilayer in
> > the water phase and let it diffuse into the bilayer. This polymer has been
> > shown to interact with the lipid bilayer in previous studies us. The issue
> > I'm having is that in my simulation the polymer stays in the water phase
> > just hovering above the lipid membrane and never interacts or diffuses.
> > I've tried simulating it in a number of different ways by varying the
> > number of water molecules, changing box size or polymer position however I
> > haven't had any success yet. The main steps in setting up my system is as
> > follows:
> > 1. Simulate the Lipid bilayer alone to equilibrate it. 2. Take the final
> > box size of the lipid bilayer and use it to place the Polymer at specific
> > point just above the lipid bilayer. 3. Perform energy minimization on the
> > system4. Perform NVT and NPT5. Run the simulation
> > Any advice would be helpful
> > Regards
> > Alex
> > --
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