[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
mariagoranovic at gmail.com
Thu Nov 5 12:09:44 CET 2009
Hello All (and especially Berk)
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?
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.
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?
Thank you so much
Technical University of Denmark
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