You can do an RMS fit and then trajout the resulting trajectory.
On Tue, Oct 26, 2010 at 10:08 AM, John S <s.john634.gmail.com> wrote:
> Dear Amber Users,
>
> I have activated nscm flag in my simulations for removal of translational
> and rotational motion.
>
> Now when i visualize my MD simulation , it appears the entire structure is
> rotating .
>
> I need to calculate the diffusion coefficient of selected residues (which
> have no bonding with other residues ), How can I post process my trajectory
> to remove this rotation before I calculate diffusion coefficient .
>
> Thanks
> John
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Oct 27 2010 - 10:30:05 PDT
