Re: problem for simulation of membrane protein system

From: Jeffrey Potoff (
Date: Tue Apr 12 2011 - 11:29:25 CDT

All kinds of things can go wrong in these kinds of simulations. You
need to make sure of the following:

1. You have enough lipids to give you the correct area per lipid.
1a. You need to have enough water to give you ~1.0 g/cm^3 in the
regions where you want water.
2. You are at conditions (T+P) where the lipid bilayers don't condense.
3. If you have ions, you need to make sure you haven't created a charge
gradient. If you have a charge gradient water will happily blow right
through your membranes.


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

Jeffrey J. Potoff               
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815

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