From: Suranga Edirisinghe (nerangedi_at_gmail.com)
Date: Tue Aug 28 2012 - 15:49:37 CDT
I think a vector has a magnitude and a direction.
On Tue, Aug 28, 2012 at 1:34 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?
> 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
> > 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
> > 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 akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
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