Modeling a polymer

From: Glenn Johnson (
Date: Thu Mar 24 2005 - 13:44:29 CST

I would like to model a polymer (cellulose) with NAMD. What I would
like to do is start with a crystal structure and make a packed
super-cell. Is there a way to do this with psfgen given the unit cell
or would I have to have to pack the cell with some other program and
produce a pdb file with all of the chains?

I will be using periodic boundary conditions. Is there a way to
covalently bond the ends of the chains across the periodic images along
the polymer axis in order to simulate a chain of infinite length?


Glenn Johnson <>
U. S. Department of Agriculture

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