Re: problem for simulation of membrane protein system

From: Giacomo Fiorin (
Date: Tue Apr 12 2011 - 11:30:39 CDT

Hello Maiti, perhaps the areas of the two bilayers have not equilibrated
yet? Have you considered running with NPT with flexibleCell, but without
fixing the area, i.e. *not* in NPzAT? The CHARMM27 lipid model may be
difficult to use with this protocol, but you can try with the newest C36
lipid model.

Also, I think you should equilibrate the bilayers before releasing the
restraints on the protein, or you may have conformational changes in it that
will be difficult or impossible to undo during the production run.

Finally, keep in mind that since you have two bilayers (both with the
protein embedded, I believe) their equilibrium areas may be different,
because you removed a different number of lipid molecules when embedding the
protein. You may try to fine-tune the number of lipid molecules in each
bilayer to minimize this.


---- ----
  Giacomo Fiorin - Postdoctoral Researcher
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
---- ----

On Tue, Apr 12, 2011 at 12:06 PM, Buddhadev Maiti <>wrote:

> Dear NAMD Users,
> I am facing problem to simulate membrane protein system. The detail
> information is in below:
> System: Two Lipid bilayers + protein + water + ions
> Force field: Charmm
> Program using for simulation: NAMD-2.7
> Simulation protocol: Energy minimization, NVT and NPT with restraining
> protein, water, ions and headgroups of lipids to compress the box and no
> undesirable gaps present between the periodic images of box, And also no
> gaps are in between lipids and protein. Then I gradually scale down the
> restraint and run for NPT constant area production run basically NPAT
> production run without any restraint. I am getting unphysical results. The
> gaps are creating between the periodic images of box basically in corners of
> the box and also in between protein and lipids. The gaps are growing
> continuously with production run and waters are entering inside the corners
> of the box and lipids tailgroups. The system is completely turned out to be
> problematic.
> Could you please give me some suggestions, it will be great help for me.
> Have a nice day,
> Thanks,
> Maiti

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