wouldn't you expect less rmsd when fitting compared to no fitting?
the fitting procedure attempts to eliminate translation and rotation of the
molecule you are fitting.
On Wed, Mar 27, 2013 at 1:17 PM, HIMANSHU JOSHI <himanshuphy87.gmail.com>wrote:
> Dear friends,
>
> I am using ptraj to calculate rmsd for amber trajectories.
> I am getting less rmsd with fit compared to
> nofit. I want to know that what algorithm rms follow
> to do this fitting of trajectories.
>
> Looking forward for your kind suggestions.
>
> --
> *With Regards,
> HIMANSHU JOSHI
> Graduate Scholar, Center for Condense Matter Theory
> Department of Physics IISc.,Bangalore India 560012*
> ॐ सर्वे भवन्तु सुखिनः सर्वे सन्तु निरामयः।
> सर्वे भद्रणिपश्यन्तु मा कश्चिद्दुःख भाग भवेत्॥
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Mar 27 2013 - 10:30:04 PDT
