I did use -pbc nojump, but that does not help<br><br>The drift is about 1 nm per 10 microseconds .<br><br>(this is a martini simulation)<br><br><div class="gmail_quote">On Thu, Nov 5, 2009 at 1:02 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 12:09 PM, maria goranovic 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;">
Hello All (and especially Berk)<br>
<br>
This is an update of the problem that I was facing earlier. I used to tau_p of 3.0 ps, and the problem does not go away, the bilayers still drifts in the simulation box. So this is probably a bug then?<br>
</blockquote></div>
How much is the drift (nm/ns)? Did you use removal of center of mass of the entire system of<br>
bilayer/solvent separately?<div class="im"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
I still cannot understand how to put the bilayer back into the center of the simulation box. As suggested by Justin, I tried to use just one tail atom of a lipid for centering, but that did not work either.<br>
<br>
I noticed that my bilayer, which is initially at the center of the simulation box, separates into two leaflets at the box edges from the very first step of the simulation itself, but i am not able to correct that using the -center and -boxcenter zero options. Can someone please make a suggestion and help?<br>
</blockquote></div>
You have to do use -pbc nojump first and then center ...<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>
Thank you so much<br>
<br>
-Maria<br>
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br></div><div class="im">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>