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.
-Justin
On Fri, Apr 12, 2013 at 6:52 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen <kieuthu2...@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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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