[gmx-users] Re: Free Energy Calculation
dmobley at gmail.com
Fri Aug 7 16:05:23 CEST 2009
On Thu, Aug 6, 2009 at 3:01 PM, Nagy, Peter I. <PNAGY at utnet.utoledo.edu>wrote:
> A question to the answer below:
> If the Berendsen barostat does not sample correctly the distribution of
> then what guarantees that the the volume/density is correct
> at the end of the equilibration phase when the user is advised to switch to
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
> Peter Nagy
> The University of Toledo
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of David Mobley
> Sent: Thu 8/6/2009 2:38 PM
> To: Mauricio Carrillo Tripp
> Cc: Discussion list for GROMACS users
> Subject: [gmx-users] Re: Free Energy Calculation
> Sorry for the delay answering. These questions are better put on the
> GROMACS users list.
> 1) Yes -- the Berendsen barostat does not sample the correct
> distribution of pressures.
> 2) Regenerating velocities is fine for a couple of reasons: (a) we are
> after thermodynamics, not dynamics, and (b) regenerating velocities
> does not de-equilibrate the system (see the Andersen thermostat, for
> On Jun 8, 2009, at 3:02 PM, Mauricio Carrillo Tripp wrote:
> > Hi,
> > I've been following directions at
> > to calculate hydration free energies of a few small molecules, and I
> > have a couple of questions:
> > 1) Is there a reason for using NVT instead of NPT for the production
> > step?
> > 2) I noticed that between the equilibration and the production runs
> > you generate velocities at each step,
> > instead of using the ones from the previous step. Is there a
> > reason for doing this? wouldn't this
> > 'de-equilibrate' an already equilibrated system?
> > Thank you.
> > --
> > 0 | Mauricio Carrillo Tripp, PhD
> > / | Department of Molecular Biology, TPC6
> > 0 | The Scripps Research Institute
> > \ | 10550 North Torrey Pines Road
> > 0 | La Jolla, California 92037
> > / | trippm at scripps.edu
> > 0 | http://www.scripps.edu/~trippm<http://www.scripps.edu/%7Etrippm>
> > ** Aut tace aut loquere meliora silentio **
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