Be aware that if you used a variety of different starting structures and if
the differences between starting structure is larger than the variation
within individual trajectories, then the PCA is going to be dominated by
the initial structures rather than the simulation dynamics. I'm not saying
that this invalidates the approach, just something to keep in mind.
On Mon, Apr 17, 2017 at 7:25 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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>
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Received on Mon Apr 17 2017 - 07:00:02 PDT
