Hi,
For RMS-fitting (default), both ptraj and cpptraj use Kabsch's
algorithm for determining the best-fit rotation matrix.
W. Kabsch, A discussion of the solution for the best rotation to
relate two sets of vectors, Acta Crystallographica A 34 (1978)
827–828.
-Dan
On Wed, Mar 27, 2013 at 11:17 AM, 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॥
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Mar 27 2013 - 10:30:03 PDT
