Re: [AMBER] PCA - concatenating trajectories

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 17 Apr 2017 09:25:47 -0400

It is legitimate, and can be a good way to assess convergence between
independent trajectories. See e.g.:

http://pubs.acs.org/doi/abs/10.1021/ct400862k
http://pubs.acs.org/doi/abs/10.1021/jp4125099

Scripts for performing "combined PCA" with cpptraj are in supporting
information.

-Dan


On Mon, Apr 17, 2017 at 9:19 AM, George Tzotzos <gtzotzos.me.com> wrote:
> This is a general question regarding PCA.
>
> Is it legitimate to concatenate independent trajectories (same complex, receptor, ligand; same topologies) and then conduct PCA on the combined trajectory?
>
> Thanks in advance for any suggestions
>
> George
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-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Apr 17 2017 - 06:30:05 PDT
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