Re: Penetration of water

From: Mauricio Carrillo Tripp (
Date: Fri Oct 07 2005 - 10:40:13 CDT

You need to add water to both sides. When you build your system
you must be careful of not having water molecules inside the protein
nor membrane, then you need to minimize and equilibrate the system.
After doing this, the water will penetrate the bilayer to some extent,
at the lipids' head group region, but this is OK. You don't need to do
anything else.

On 10/7/05, bo baker <> wrote:
> Hello, NAMD:
> I try to build up a system containing a protein, lipid bilayer and
> water box. I would like to suject the system to MD simulation with
> periodic boundary condition. The protein is only half-way through the
> membrane. I am more interested at the conformations of the cytoplasm
> part of the protein. The first question, can I just add water on one
> side of the membrane? If not, I need to add waters at both sides of
> the membrane. So the second question is how can I prevent the penation
> of water through the lipid bilayer ? Some papers suggested to add an
> opposing force to water molecules. How can I tell NAMD to do this?
> Thank you for help. I use NAMD 2.6.1.
> Bo

Mauricio Carrillo Tripp, PhD
Department of Chemistry
Wabash College

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