Centering on one atom has a problem that the lipid diffuses in the plane of the membrane, and as a result, the entire system starts to center around the lipid resulting in a simulation box which translates a lot in the bilayer plane. <br>
<br>The splitting is not a problem, yes. But during the simulation period when the bilayer is not split, it diffuses quite a bit along the bilayer normal (after use of -pbc mol, and centering around the lipid center of mass). a plot of the lipid center of mass shows the bilayer diffusing along z, when its not split.<br>
<br><div class="gmail_quote">On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I did use -pbc nojump, but that does not help<br>
</blockquote>
<br>
What about entering on a central lipid tail atom, I suggested some time ago? The bilayer probably just splits across periodic boundaries, so this is not really a problem; just a visualization artefact.<br>
</blockquote></div>
The splitting is not a problem and I think that centering using one lipid (tail) won't change the problem if<br>
the bilayer is cut half! Or the -pbc mol should be applied ...<div><div></div><div class="h5"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The drift is about 1 nm per 10 microseconds .<br>
(this is a martini simulation)<br>
On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole <<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a> <mailto:<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>>> wrote:<br>
On Nov 5, 2009, at 12:09 PM, maria goranovic wrote:<br>
Hello All (and especially Berk)<br>
This is an update of the problem that I was facing earlier. I<br>
used to tau_p of 3.0 ps, and the problem does not go away, the<br>
bilayers still drifts in the simulation box. So this is<br>
probably a bug then?<br>
How much is the drift (nm/ns)? Did you use removal of center of mass<br>
of the entire system of<br>
bilayer/solvent separately?<br>
I still cannot understand how to put the bilayer back into the<br>
center of the simulation box. As suggested by Justin, I tried to<br>
use just one tail atom of a lipid for centering, but that did<br>
not work either.<br>
I noticed that my bilayer, which is initially at the center of<br>
the simulation box, separates into two leaflets at the box edges<br>
from the very first step of the simulation itself, but i am not<br>
able to correct that using the -center and -boxcenter zero<br>
options. Can someone please make a suggestion and help?<br>
You have to do use -pbc nojump first and then center ...<br>
Thank you so much<br>
-Maria<br>
-- Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>