Penetration of water

From: bo baker (bo.bybaker_at_gmail.com)
Date: Fri Oct 07 2005 - 00:20:46 CDT

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

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