[gmx-users] lipid bilayer separation

[Felipe Merino]

Hey

I think the problem he is having is that the leaflets are being pulled 
apart at the beginning of the run. You should place some positional 
restraints on the

direction perpendicular to the membrane (I'd bet it's the z component). 
A restraint on one atom of each lipid will allow the system to fill the 
vacuum that you

most likely introduced during system preparation.

Felipe

On 05/07/16 14:50, Justin Lemkul wrote:
>
>
> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 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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-- 
Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2315