>
>
>
> Message: 5
> Date: Tue, 19 Oct 2010 13:06:42 -0400
> From: "Justin A. Lemkul" <[email protected]>
> Subject: Re: [gmx-users] Re: Umbrella sampling with temperature and
> pressure coupling method problem (Justin A. Lemkul)
> To: Discussion list for GROMACS users <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> DeChang Li wrote:
> >
> >
> >
> > Message: 6
> > Date: Tue, 19 Oct 2010 09:30:47 -0400
> > From: "Justin A. Lemkul" <[email protected] <mailto:[email protected]>>
> > Subject: Re: [gmx-users] Umbrella sampling with temperature and
> > pressure coupling method problem
> > To: Discussion list for GROMACS users <[email protected]
> > <mailto:[email protected]>>
> > Message-ID: <[email protected] <mailto:[email protected]
> >>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > [email protected] <mailto:[email protected]> 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?
> >
>
> I would think that a proper statistical mechanical ensemble would be
> considered
> indispensable for any simulation. In my mind, there is no real reason to
> use
> less accurate methods when collecting data. If your goal is a comparison
> of
> methods, or consistency with other results, sure, then you may have a
> reason to
> use algorithms that may be less than optimal. For any sensitive
> thermodynamic
> study, I would strongly argue that your potential energy surface needs to
> be
> rigorously correct.
>
> The point is this. You have to defend your choices to a skeptical audience
> (reviewers). This is one question that might be asked, and really should
> be.
> Methods should be scrutinized. So I would ask you this: why perform your
> simulations with algorithms that are not as accurate as others, when those
> better algorithms are accessible to you and do not harm performance in any
> demonstrable way?
>
> -Justin
>
Thank you for your reply! So I will use Nose-Hoover for temperature
coupling and Parrinello-Rahman for pressure coupling in the data collection.
Anyway, I may do some simulations with Berendsen method to see if there is
any difference in results when using the two coupling methods.
>
> >
> >
> > -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 <http://vt.edu> | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> >
> >
>
> --
> ========================================
>
> 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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