Re: Alignment

From: Axel Kohlmeyer (
Date: Thu Sep 04 2014 - 07:53:23 CDT

On Thu, Sep 4, 2014 at 2:12 PM, Zeinab Emami <> 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
NAMD list.

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


> Best,
> Zeinab

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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