Building crystal polymer

From: Shaikh Abdul Rajjak (
Date: Fri May 17 2013 - 00:59:09 CDT

Dear NAMD User,

I am new user to NAMD. I would like to build a polymer membrane (ex.
polyethylene difluoride). PVDF membrane is semicrystalline. I have build
a unit cell for PVDF and replicated it 10X10X10 using
replicateCrystal.tcl script. I have created a topology file and
parameter file based on PET tutorial. Please see the attached file for
the same. Now I would like to add bond between each monomer so that it
will be polymer and then truncate the terminal residues. I can define
bond manually but system is big. There is any way to add bond between
two monomers. I am unable to generate psf file using autopsf utility in
VMD. I want to do molecular dynamics simulation using NAMD and then
study polymer membrane biomolecular interactions.
Thank you
Abdul Rajjak

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