Anytime you are calculating a free energy, you should look to do canonical
sampling
(as well as making sure your results are converged). For very large systems,
(since NVT -> NVE) you may be able to get away with Berendsen.
I should also note that Hummer et al showed that if you do any sort of
replica exchange
with a non-canonical thermostat, your results will get corrupted.
Hope that helps!
--Dan
On Wed, Oct 20, 2010 at 12:29 AM, DeChang Li <li.dc06.gmail.com> wrote:
> 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?
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sindhikara.gmail.com
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 19 2010 - 17:30:03 PDT
