Peter,<br><br><br><br><div class="gmail_quote">On Thu, Aug 6, 2009 at 3:01 PM, Nagy, Peter I. <span dir="ltr"><<a href="mailto:PNAGY@utnet.utoledo.edu">PNAGY@utnet.utoledo.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
<br>
<p><font size="2">A question to the answer below:<br>
<br>
If the Berendsen barostat does not sample correctly the distribution of pressures<br>
then what guarantees that the the volume/density is correct<br>
at the end of the equilibration phase when the user is advised to switch to<br>
NVT?<br>
</font></p></div></blockquote><div><br>Very good question. In fact, nothing. More recently, we do an affine transformation to rescale the box size to the correct (average) box size at the end of NPT equilibration and then run a short additional NVT eqiulibration before NVT production. However, this tends not to work well for systems containing large molecules such as proteins. Ideally I would instead have a barostat that samples the proper distribution of pressures to use!<br>
<br>David<br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><p><font size="2"><br>
Peter Nagy<br>
The University of Toledo<div><div></div><div class="h5"><br>
<br>
-----Original Message-----<br>
From: <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> on behalf of David Mobley<br>
Sent: Thu 8/6/2009 2:38 PM<br>
To: Mauricio Carrillo Tripp<br>
Cc: Discussion list for GROMACS users<br>
Subject: [gmx-users] Re: Free Energy Calculation<br>
<br>
Hi,<br>
<br>
Sorry for the delay answering. These questions are better put on the <br>
GROMACS users list.<br>
<br>
1) Yes -- the Berendsen barostat does not sample the correct <br>
distribution of pressures.<br>
2) Regenerating velocities is fine for a couple of reasons: (a) we are <br>
after thermodynamics, not dynamics, and (b) regenerating velocities <br>
does not de-equilibrate the system (see the Andersen thermostat, for <br>
example).<br>
<br>
<br>
<br>
On Jun 8, 2009, at 3:02 PM, Mauricio Carrillo Tripp wrote:<br>
<br>
> Hi,<br>
><br>
> I've been following directions at <a href="http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial" target="_blank">http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial</a><br>
> to calculate hydration free energies of a few small molecules, and I <br>
> have a couple of questions:<br>
> 1) Is there a reason for using NVT instead of NPT for the production <br>
> step?<br>
> 2) I noticed that between the equilibration and the production runs <br>
> you generate velocities at each step,<br>
> instead of using the ones from the previous step. Is there a <br>
> reason for doing this? wouldn't this<br>
> 'de-equilibrate' an already equilibrated system?<br>
><br>
> Thank you.<br>
><br>
> --<br>
> 0 | Mauricio Carrillo Tripp, PhD<br>
> / | Department of Molecular Biology, TPC6<br>
> 0 | The Scripps Research Institute<br>
> \ | 10550 North Torrey Pines Road<br>
> 0 | La Jolla, California 92037<br>
> / | <a href="mailto:trippm@scripps.edu" target="_blank">trippm@scripps.edu</a><br>
> 0 | <a href="http://www.scripps.edu/%7Etrippm" target="_blank">http://www.scripps.edu/~trippm</a><br>
><br>
> ** Aut tace aut loquere meliora silentio **<br>
<br>
<br>
</div></div></font>
</p>
</div>
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