[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

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 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  
> 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
> ** Aut tace aut loquere meliora silentio **

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