Dear Elisa,
Sorry if I misunderstand the question...I don't know the details of REMD, but why couldn't we just use the "rmsd" command in cpptraj? It has a "previous" option to align current frame to its previous
frame, or whatever frame if using "ref #" according to the manual.
Thanks and best wishes,
Xing
On 07/24/2017 03:59 PM, Elisa Pieri wrote:
> Hello,
>
> I have a curiosity: I have a nc trajectory obtained from REMD, so the
> frames are actually not-consecutive snapshots. Is there a tool to align the
> protein from frame to frame?
>
> I'm performing cluster analysis on it, and would like to be sure that this
> issue is not a problem in calculating RMS and average structures. Right
> now, average structures are completely unrealistic.
>
> Suggestions?
>
> Elisa
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Received on Mon Jul 24 2017 - 14:30:03 PDT
