Re: simulation of non-rectangular surface

From: Axel Kohlmeyer (
Date: Tue Aug 28 2012 - 10:39:07 CDT

On Tue, Aug 28, 2012 at 5:20 PM, Jacqueline Schmidt
<> wrote:
> 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

none. the initial simulation cell vectors are given in the NAMD conf file.

a psf has no coordinate or cell information at all.


> please make a comment (or if you could kindly send an example) of a
> non-rectangular system set up?
> Thanks
> Jackie

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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