From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Sep 04 2014 - 07:53:23 CDT
On Thu, Sep 4, 2014 at 2:12 PM, Zeinab Emami <zemami_at_ku.edu.tr> wrote:
> Dear NAMD experts,
> We need to align our trajectory file to the frame 1. I found below
> instructions for doing this:
> 1. load PSF file and DCD files.
> 2.extension: RMSD trajectory tools
> 3.Check frame 1 [instead of 0]
> 4. select the molecules [psf file] in the left down part
> 5. click align
> 6. close
> 7. save the xyz trajectory file.
> When I follow this procedure, I get a new trajectory file with elements
> which are changed a very very tiny amount.
> I am not sure if I am doing alignment in a right way or not. I appreciate
> your advice in advance.
since this is almost entirely a question about a VMD plugin, you
should post your question about this to the VMD mailing list, not the
however, before your do that, you should also work on reformulating
your question a bit. there is not just "the alignment". alignment
always has to be done relative to something. so it is not really
possible to give you a complete answer to your inquiry in its current
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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