Thank you for your reply!
Actually, my question is whether the correct canonical ensemble important
(or indispensable) for umbrella sampling?
2010/10/19 Daniel Sindhikara <sindhikara.gmail.com>
> 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 - 08:30:04 PDT
