[gmx-users] Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul)

[DeChang Li]

> Message: 6
> Date: Tue, 19 Oct 2010 09:30:47 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Umbrella sampling with temperature and
>        pressure        coupling method problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CBD9D87.6080404 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> chris.neale at utoronto.ca wrote:
> > Use Langevin dynamics (the sd integrator) to control the temperature.
> > You are sure to get the correct ensemble that way and if you are doing
> > US then you can not extract dynamics anyway.
> >
> > Hopefully somebody else can address the pressure coupling for you, but
> > probably you need to provide more information to get a useful answer
> there.
> >
>
> The Berendsen barostat suffers from the same limitations as the thermostat
> - the
> pressure distribution does not produce a true NPT ensemble.
>

   Whether the correct canonical ensemble (NPT or NVT) is important (or
indispensable) for umbrella sampling? If I used the weak coupling method
(Berendsen) to do the simulations, can I extract the PMF from the umbrella
sampling simulations?


>
> -Justin
>
> > -- original message --
> >
> > 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?
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
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