[gmx-users] Polymer not diffusing into membrane

Wed Aug 13 16:21:53 CEST 2014

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
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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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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>> Gromacs Users mailing list
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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

==================================================