Hi, Chunli
I don't get what you want to do.
For the RMSD as collective variable, just include the index of the atoms
you want to
include and the reference coordinates of those atoms, and the aligning will
be automatic
to calculate the RMSD.
Best
Feng
On Thu, Aug 24, 2017 at 3:57 PM, Chunli Yan <utchunliyan.gmail.com> wrote:
> Hello,
>
> I want to create a collective variable by RMSD. But the RMSD has to
> calculate based on one part of the protein after aligning the other part of
> the protein.
>
> Is there a way to do that?
>
> Thanks,
>
> Best,
>
>
> *Chunli*
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--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Sun Aug 27 2017 - 21:30:02 PDT
