[gmx-users] bilayer leaflets separating

Amadeu akwsum at gmail.com
Fri Nov 12 04:03:52 CET 2004

I am experiencing something very strange: the leaflets of my bilayer
are continuosly separating, thus creating a large gap in the middle of
the bilayer. I ran the simulation for 100 ps and the gap was about 10
nm. I tried this same simulation many times, in several machines, and
I cannot get it to be stable. Would anyone have any idea what may be
the problem? This is a simulation for a small bilayer with 64 and 3846
water molecules (from Tieleman's webiste). The simulation are in the
NPT ensemble (1 bar and 323 K), with 1.0 nm and 1.8 nm cut-off for the
LJ and eletrostatic interactions, respectively. Periodic conditions in
all directions. The initial velocity were generated at the start of
the simulation. I am using the GROMOS forcefile for the lipid and SPC
water. The strangest thing is that I can use this same forcefield and
conditions for the simulation of a large bilayer (128) and I do not
encounter this problem. I would greatly appreciate input/comments.



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