psf file for zeolite-water system

From: Ozgur YAZAYDIN (yazaydin_at_WPI.EDU)
Date: Sun Feb 22 2004 - 21:21:03 CST

 Dear NAMD users;

 I am a new NAMD user. I am trying to do MD simulations for water
molecules confined in Zeolite pores. Zeolite is basicly a network of SiO2
molecules. I created a pdb file for my water zeolite system successfuly,
well that was the easy part. I know Si atom is not supported by Charmm
topology file. So I cant create a psf file. Zeolite structure has only
nonbonded interactions with water molecules. How should I modify the
topology file? How can I use psfgen tool to create a psf file for this
system? or should I forget NAMD for this system?

Any advice would be appreciated.

Research Assistant
Department of Chemical Engineering
Worcester Polytechnic Institute
100 Institute Road, Worcester, MA 01609-2280

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