Inquiry about lipid membrane simulation

From: Mo Chen (
Date: Tue Jun 17 2014 - 20:57:59 CDT

Dear NAMD developers and users,

I am simulating a lipid bilayer system containing a partially embedded
protein, and am trying to convert the CHARMM input files into NAMD
configuration files.

I have two questions:

1) In CHARMM, the MMFP GEO PLANE ... is used to keep the non-crystal water
molecules away from entering the hydrophobic core of lipid bilayer, and I
wonder if there is any corresponding command lines in NAMD? I found the
NAMD tutorial about membrane system is using a tcl file and since it uses
CHARMM27 lipid force field, I figured it was created way back. Therefore, I
want to ask if there might be any update in the NAMD code that allows
restraining water with simple script lines?

2) Similar to the first question, may I ask if there is any MMFP GEO
Cylindrical .... in NAMD?

Thank you very much.


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