Berk,<br><br><div class="gmail_quote"><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>I guess the best proper solution would be to use a Parrinello-Rahman barostat.<br>
But in Gromacs this is currently not implemented in a reversible way.<br></div></blockquote><div><br>Yes, I would love to see a barostat that samples the correct distribution.<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><br>In practice I think the issues with the Berendsen thermostat are not relevant.<br>It does not generate the correct pressure and volume fluctuations,<br>but the average pressure and volume are correct. The effects of incorrect<br>
fluctuations is negligible and is surely much smaller than simulating at the wrong<br>volume, which can have a large effect on solvation free energies.<br></div></blockquote><div><br>It seems fairly like you are right (assuming your first line is meant to refer to the Berendsen barostat), but I think no one knows for sure at this point whether it matters and when it might matter. I agree that simulating at an incorrect volume can be a big problem, however. This is unlikely, but can happen, which is why we now do the affine transformation I just mentioned when looking at solvation free energies. <br>
<br>Anyway -- I'd just like to see a proper barostat implemented at some point, then the paranoid (like me) can run with a proper barostat instead of worrying about whether or not this matters, AND someone could test whether observables they are interested in come out different depending on the choice of barostat.<br>
<br>David<br><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><br>I also think that issues with Berendsen pressure coupling are much less severe<br>
than the issues with Berendsen temperature coupling. Berendsen tcoupl can have<br>significant effects on your ensemble. But in Gromacs 4.0 this can easily be avoided<br>by using the v-rescale thermostat.<br><br>Berk<br><br>
<hr>Subject: RE: [gmx-users] Re: Free Energy Calculation<br>Date: Thu, 6 Aug 2009 16:01:04 -0400<br>From: <a href="mailto:PNAGY@UTNet.UToledo.Edu" target="_blank">PNAGY@UTNet.UToledo.Edu</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><div>
<div class="h5"><br><br>
<br>
<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>
<br>
Peter Nagy<br>
The University of Toledo<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>
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