[gmx-users] bilayer leaflets separating

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Fri Nov 12 11:06:12 CET 2004

Hi all, 

On Friday 12 November 2004 04:03, Amadeu wrote:
> 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.

Think you got the same problem like me, i think the following posting could 
solve your problem if it^s pbc problem




 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de

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