[gmx-users] Polymer not diffusing into membrane

Alex s as1783 at hotmail.com
Wed Aug 13 16:46:06 CEST 2014 

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 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 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 box.
ThanksAlex

> Date: Wed, 13 Aug 2014 10:21:42 -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, 10:45 PM, Alex s wrote:
> > http://www.mediafire.com/view/63k3pi3k3hahnu3/snapshots(2).docxhttp://www.mediafire.com/view/02dk2kwj6tec939/mdp.txt
> > hope this helps
> 
> Note the massive change in your box along z.  Something has gone terribly wrong 
> in the simulation.  Is your unit cell properly filled with water?  Do you notice 
> anything else bizarre going on?
> 
> -Justin
> 
> >
> > Date: Tue, 12 Aug 2014 21:58:09 -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, 9:50 PM, Alex s wrote:
> >>> 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.
> >>
> >> Post images (and any other files, for that matter) to file-sharing services and
> >> provide the links.
> >>
> >> -Justin
> >>
> >>> Thanks
> >>> Alex
> >>>
> >>>> 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.
> >>>>
> >>>> -Justin
> >>>>
> >>>>>> 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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> >>>>>     		 	   		
> >>>>>
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> >>>> --
> >>>> ==================================================
> >>>>
> >>>> Justin A. Lemkul, Ph.D.
> >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>>
> >>>> Department of Pharmaceutical Sciences
> >>>> School of Pharmacy
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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
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
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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
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
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