[gmx-users] pbc problem

[Justin Lemkul]

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

-- 

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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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