[gmx-users] bilayer leaflets separating
akwsum at gmail.com
Fri Nov 12 13:21:48 CET 2004
Tsjerk and Florian,
Thank you for your comments. When I do apply the "-pbc nojump" option,
I do get the bilayer to visually look correct, but what concerns me
is that the Z-dimension (normal to the bilayer interface) is very
large and does not seem to stabilize. The bilayer and water are only
about 10 nm, but box size is about 20 nm and its continues to increase
as through the simulation. Is this what you have observed too? Any
idea why the box size in the z-dimension expands like that?
On Fri, 12 Nov 2004 10:34:39 +0100, Tsjerk Wassenaar
<t.a.wassenaar at chem.rug.nl> wrote:
> 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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> -- :)
> -- :) Tsjerk A. Wassenaar, M.Sc.
> -- :) Molecular Dynamics Group
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