[gmx-users] lipid bilayer separation

[Justin Lemkul]

On 7/5/16 8:48 AM, xy21hb wrote:
> Dear Mark,
>
> I have trjconv -pbc mol, so the PBC has been considered.
> But still, the system seems out of order, as shown,
>

No one is seeing any images because the list does not accept attachments. 
Please upload an image somewhere and provide a URL.

-Justin

> Thanks,
>
> Yao
>
>
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>
>
>
>
>
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> At 2016-07-05 20:36:33, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>> Hi,
>>
>> The bilayer can't split up. That would make no physical sense. The
>> representation you visualized can be different from your expectation
>> however.
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>>
>> Mark
>>
>> On Tue, Jul 5, 2016 at 1:50 PM xy21hb <xy21hb at 163.com> wrote:
>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Dear all, I have a simple lipid bilayer system, POPC in water built up
>>> with charmm GUI. Now I just want to add more water on each side of the
>>> lipid, as shown in the attachment. However, when I energy minimize and
>>> equilibrate it, the bilayer split up. Any guess on the reason? Many thanks,
>>> Yao--
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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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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