[gmx-users] Re: Free Energy Calculation
Nagy, Peter I.
PNAGY at UTNet.UToledo.Edu
Thu Aug 6 22:01:04 CEST 2009
A question to the answer below:
If the Berendsen barostat does not sample correctly the distribution of pressures
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
The University of Toledo
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:
> I've been following directions at http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial
> 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
> 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
> ** Aut tace aut loquere meliora silentio **
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users