The fact that you are doing umbrella sampling has no effect on which
thermostat you should use.
I don't believe Nose-hoover is implemented in AMBER. I'd recommend Langevin
since it can
provide canonical results. Check the AMBER manual for more info on the
thermostats.
--Dan
On Tue, Oct 19, 2010 at 9:57 PM, DeChang Li <li.dc06.gmail.com> wrote:
> Dear all,
>
> I want to use umbrella sampling to calculate the PMF of the
> conformational transition of a protein. What temperature coupling method
> and
> pressure coupling method should I use? Berendsen temperature coupling or
> Nose-Hoover temperature coupling? Or each one is OK?
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>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Tue Oct 19 2010 - 08:30:03 PDT
