[gmx-users] Polymer not diffusing into membrane
as1783 at hotmail.com
Wed Aug 13 03:50:49 CEST 2014
I think that may well be the case. The polymer would move freely towards and away from the bilayer in the Z direction but would never diffuse or get close enough to interact. I've just run a simulation placing the polymer in a tight space with a bilayer above and below it and theres barely any movement of the polymer along the Z axis, its seems that there's something 'repelling' it any time it gets close to the bilayer. I've attached a text version of my mdp file, I would like to attach snapshots of my system setup but it would exceed the 50 KB limit.
> Date: Tue, 12 Aug 2014 17:15:25 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Polymer not diffusing into membrane
> On 8/12/14, 1:35 PM, Alex s wrote:
> > I've run it for 200 ns which I think is long enough allow the polymer to diffuse.
> If, as you say, it "never interacts or diffuses," it suggests that you're
> applying some sort of restraint. Without seeing .mdp files and some sort of
> quantitative measure of what you're seeing, it's hard to comment further.
> Images would also be helpful. It depends on the size of the system and the
> initial distance, but I would think you'd need far less than 200 ns to see such
> an interaction.
> >> 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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> 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
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> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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