[gmx-users] lipid bilayer separation

[xy21hb]

Dear Mark,

I have trjconv -pbc mol, so the PBC has been considered.
But still, the system seems out of order, as shown,

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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