[gmx-users] Re: Free Energy Calculation

[David Mobley]

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.

>
> 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.

David



> 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.
>
> Berk
>
> ------------------------------
> 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
> NVT?
>
> 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
>
> Hi,
>
> 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
> example).
>
>
>
> 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<http://www.scripps.edu/%7Etrippm>
> >
> > ** Aut tace aut loquere meliora silentio **
>
>
>
>
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