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Message: 6<br>
Date: Tue, 19 Oct 2010 09:30:47 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Umbrella sampling with temperature and<br>
pressure coupling method problem<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4CBD9D87.6080404@vt.edu">4CBD9D87.6080404@vt.edu</a>><br>
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<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a> wrote:<br>
> Use Langevin dynamics (the sd integrator) to control the temperature.<br>
> You are sure to get the correct ensemble that way and if you are doing<br>
> US then you can not extract dynamics anyway.<br>
><br>
> Hopefully somebody else can address the pressure coupling for you, but<br>
> probably you need to provide more information to get a useful answer there.<br>
><br>
<br>
The Berendsen barostat suffers from the same limitations as the thermostat - the<br>
pressure distribution does not produce a true NPT ensemble.<br></blockquote><div><br></div><div> 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?</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
-Justin<br>
<br>
> -- original message --<br>
><br>
> Dear all,<br>
><br>
> I want to use umbrella sampling to calculate the PMF of the<br>
> conformational transition of a protein. What temperature coupling method<br>
> and<br>
> pressure coupling method should I use? Berendsen temperature coupling or<br>
> Nose-Hoover temperature coupling? Or each one is OK?<br>
><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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