DeChang Li wrote:
Message: 6
Date: Tue, 19 Oct 2010 09:30:47 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Umbrella sampling with temperature and
pressure coupling method problem
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4cbd9d87.6080...@vt.edu <mailto:4cbd9d87.6080...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
chris.ne...@utoronto.ca <mailto:chris.ne...@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
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
