[gmx-users] Re: Free Energy Calculation

Berk Hess gmx3 at hotmail.com
Fri Aug 7 10:44:25 CEST 2009

Good question.

I guess the best proper solution would be to use a Parrinello-Rahman barostat.
But in Gromacs this is currently not implemented in a reversible way.

In practice I think the issues with the Berendsen thermostat are not relevant.
It does not generate the correct pressure and volume fluctuations,
but the average pressure and volume are correct. The effects of incorrect
fluctuations is negligible and is surely much smaller than simulating at the wrong
volume, which can have a large effect on solvation free energies.

I also think that issues with Berendsen pressure coupling are much less severe
than the issues with Berendsen temperature coupling. Berendsen tcoupl can have
significant effects on your ensemble. But in Gromacs 4.0 this can easily be avoided
by using the v-rescale thermostat.


Subject: RE: [gmx-users] Re: Free Energy Calculation
Date: Thu, 6 Aug 2009 16:01:04 -0400
From: PNAGY at UTNet.UToledo.Edu
To: gmx-users at gromacs.org

RE: [gmx-users] Re: Free Energy Calculation

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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