simulation of non-rectangular surface

From: Jacqueline Schmidt (
Date: Tue Aug 28 2012 - 10:20:02 CDT

Dear NAMD users,
I have car/mdf files of a non-rectangular clay surface which I want to run with NAMD. I know how to make the pdb and psf files for the rectangular systems but I wonder which modifications and in which files (pdb or psf or conf) I have to make in order to run non-rectangular system. Can anyone please make a comment (or if you could kindly send an example) of a non-rectangular system set up?

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:57 CST