[gmx-users] Polymer not diffusing into membrane

[Alex s]

http://www.mediafire.com/view/63k3pi3k3hahnu3/snapshots(2).docxhttp://www.mediafire.com/view/02dk2kwj6tec939/mdp.txt
hope this helps
> 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
> >>>>> --
> >>>>> Gromacs Users mailing list
> >>>>>
> >>>>> * Please search the archive at
> >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>>>> posting!
> >>>>>
> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>
> >>>>> * For (un)subscribe requests visit
> >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
> >>>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> >>>>
> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>
> >>>> * For (un)subscribe requests visit
> >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> >>>    		 	   		
> >>>
> >>
> >> --
> >> ==================================================
> >>
> >> 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
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> >   		 	   		   		 	   		
> >
> >
> >
> 
> -- 
> ==================================================
> 
> 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
> 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.