[gmx-users] Re: Free Energy Calculation

Floris Buelens floris_buelens at yahoo.com
Fri Aug 7 16:32:33 CEST 2009

Hi David and Berk,

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.

> Yes, I would love to see a barostat that samples the correct distribution.

Can you clarify? The wording in the manual implies that Parrinello-Rahman coupling samples the correct distribution... When you say it's not reversible do I understand right that means you can't run your simulation backwards and get an identical result, if yes, is this ever relevant in practice for e.g. solvation free energy calculation? David, why don't you use Parrinello-Rahman coupling?


>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.

It seems fairly like you are right (assuming your first line is meant to refer to the Berendsen barostat), but I think no one knows for sure at this point whether it matters and when it might matter. I agree that simulating at an incorrect volume can be a big problem, however. This is unlikely, but can happen, which is why we now do the affine transformation I just mentioned when looking at solvation free energies. 
Anyway -- I'd just like to see a proper barostat implemented at some point, then the paranoid (like me) can run with a proper barostat instead of worrying about whether or not this matters, AND someone could test whether observables they are interested in come out different depending on the choice of barostat.


>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
>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 **
What can you do with the new Windows Live? Find out
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