[gmx-users] bilayer leaflets separating

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Fri Nov 12 10:34:39 CET 2004

Hi Amadeu,

Are you by chance observing the jumping across the periodic boundary? 
That's only a virtual thing.
Try running the trajectory through trjconv with the '-pbc nojump' option.


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.
>                --Amadeu
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>gmx-users at gromacs.org
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