From: Zeinab Emami (
Date: Thu Sep 04 2014 - 07:12:14 CDT

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.


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