<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
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Message: 5<br>
Date: Tue, 19 Oct 2010 13:06:42 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: Umbrella sampling with temperature and<br>
pressure coupling method problem (Justin A. Lemkul)<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:4CBDD022.6020505@vt.edu">4CBDD022.6020505@vt.edu</a>><br>
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DeChang Li wrote:<br>
><br>
><br>
><br>
> 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> <mailto:<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>
> <mailto:<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> <mailto:<a href="mailto:4CBD9D87.6080404@vt.edu">4CBD9D87.6080404@vt.edu</a>>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
><br>
><br>
> <a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a> <mailto:<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<br>
> doing<br>
> > US then you can not extract dynamics anyway.<br>
> ><br>
> > Hopefully somebody else can address the pressure coupling for<br>
> you, but<br>
> > probably you need to provide more information to get a useful<br>
> answer there.<br>
> ><br>
><br>
> The Berendsen barostat suffers from the same limitations as the<br>
> thermostat - the<br>
> pressure distribution does not produce a true NPT ensemble.<br>
><br>
><br>
> Whether the correct canonical ensemble (NPT or NVT) is important (or<br>
> indispensable) for umbrella sampling? If I used the weak coupling method<br>
> (Berendsen) to do the simulations, can I extract the PMF from the<br>
> umbrella sampling simulations?<br>
><br>
<br>
I would think that a proper statistical mechanical ensemble would be considered<br>
indispensable for any simulation. In my mind, there is no real reason to use<br>
less accurate methods when collecting data. If your goal is a comparison of<br>
methods, or consistency with other results, sure, then you may have a reason to<br>
use algorithms that may be less than optimal. For any sensitive thermodynamic<br>
study, I would strongly argue that your potential energy surface needs to be<br>
rigorously correct.<br>
<br>
The point is this. You have to defend your choices to a skeptical audience<br>
(reviewers). This is one question that might be asked, and really should be.<br>
Methods should be scrutinized. So I would ask you this: why perform your<br>
simulations with algorithms that are not as accurate as others, when those<br>
better algorithms are accessible to you and do not harm performance in any<br>
demonstrable way?<br>
<br>
-Justin<br></blockquote><div><br></div><div> 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.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
><br>
><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<br>
> method<br>
> > and<br>
> > pressure coupling method should I use? Berendsen temperature<br>
> 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> <<a href="http://vt.edu" target="_blank">http://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>
><br>
> ========================================<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>
<br>
========================================<br>
<br>
<br></blockquote></div>