[gmx-users] pbc problem

Justin Lemkul jalemkul at vt.edu
Mon Apr 15 12:02:33 CEST 2013

On 4/14/13 11:21 PM, Kieu Thu Nguyen wrote:
> Thank Justin !
> I used the command "editconf -center" and i saw my membrane was in center
> of the box. I am stupid in that how putting the bilayer in a periodic image
> (instead between two periodic images as it was).
> Can you give me some instructions ?
> Many thanks !

I don't know what it is that you did before, so I can't say.  In principle, one 
could have two leaflets at periodic boundaries along the z-axis and it's exactly 
the same as having an intact membrane in the center of the box from the 
standpoint of dynamics.  For building membrane protein systems, however, that's 
less than convenient.


> On Fri, Apr 12, 2013 at 6:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen <kieuthu2212 at gmail.com
>>> wrote:
>>> Dear All,
>>> I made a POPC bilayer and carried out embedding a protein into this
>>> membrane. But the fatal error has appeared :
>>> Fatal error:
>>> Something is wrong with your membrane. Max and min z values are 12.342000
>>> and 0.016000. Maybe your membrane is not centered in the box, but located
>>> at the box edge in the z-direction, so that one membrane is distributed
>>> over two periodic box images. Another possibility is that your water
>> layer
>>> is not thick enough.
>>> I think my bilayer stay at between two periodic images. What should i do
>> to
>>> put it in corrected position ?
>> It should be a very simple matter of visualization. Use editconf -center to
>> place the membrane wherever you want within the unit cell. You can remove
>> the uncertainty ("I think" is weak compared to "I know") by looking at the
>> box vectors and then numerically determining the center of the membrane
>> with g_traj. That should provide you with all the information you need to
>> determine what's going on.
>> -Justin
>> --
>> ========================================
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540)
>> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> ========================================
>> --
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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