<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="MS Exchange Server version 6.5.7654.12">
<TITLE>RE: [gmx-users] Re: Free Energy Calculation</TITLE>
</HEAD>
<BODY>
<!-- Converted from text/plain format -->
<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>
<BR>
Peter Nagy<BR>
The University of Toledo<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org 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">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>
> / | trippm@scripps.edu<BR>
> 0 | <A HREF="http://www.scripps.edu/~trippm">http://www.scripps.edu/~trippm</A><BR>
><BR>
> ** Aut tace aut loquere meliora silentio **<BR>
<BR>
<BR>
</FONT>
</P>
</BODY>
</HTML>