[gmx-users] pbc problem
Kieu Thu Nguyen
kieuthu2212 at gmail.com
Mon Apr 15 05:21:45 CEST 2013
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 !
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
> > 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
> > is not thick enough.
> > I think my bilayer stay at between two periodic images. What should i do
> > 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
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