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

[DeChang Li]

>
>
>
> Message: 5
> Date: Tue, 19 Oct 2010 13:06:42 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Umbrella sampling with temperature and
>        pressure        coupling method problem (Justin A. Lemkul)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CBDD022.6020505 at vt.edu>
> 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" <jalemkul at vt.edu <mailto: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
> >     <mailto:gmx-users at gromacs.org>>
> >     Message-ID: <4CBD9D87.6080404 at vt.edu <mailto:4CBD9D87.6080404 at vt.edu
> >>
> >     Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> >     chris.neale at utoronto.ca <mailto: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?
> >
>
> 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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