Re: simulation of non-rectangular surface

From: Jacqueline Schmidt (
Date: Tue Aug 28 2012 - 15:34:50 CDT

Thanks Axel for your response. Apart from cellBasisVectorX (X=1,2. or 3) by which the box lengths are added (in the namd configuration file) I can not find any command for including the cell angles! Am I missing it?  Thanks, Jackie ________________________________ From: Axel Kohlmeyer <> To: Jacqueline Schmidt <> Cc: namd <> Sent: Tuesday, August 28, 2012 11:39 AM Subject: Re: namd-l: simulation of non-rectangular surface 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. axel. > 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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