From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 28 2012 - 16:00:16 CDT
On Tue, Aug 28, 2012 at 10:34 PM, Jacqueline Schmidt
> 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?
each vector is a cartesian vector in space.
this is more general and angles don't need to be specified.
> Thanks, Jackie
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: Jacqueline Schmidt <jacqueline_schmidt_1983_at_yahoo.com>
> Cc: namd <namd-l_at_ks.uiuc.edu>
> 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
> <jacqueline_schmidt_1983_at_yahoo.com> 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?
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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