[gmx-developers] Re: gmx-developers Digest, Vol 16, Issue 16
Michael Shirts
mrshirts at gmail.com
Thu Aug 11 19:23:26 CEST 2005
Hi, all-
Obviously this is getting to be quite confusing. I'll volunteer to
head up a "examine thermostat and barostat" squad to try to get best
practices in the next version of gromacs -- I've worked with the
current version fairly extensively trying new things out (though there
is obviously much more I need to try!). I'll be pretty busy up
through the end of ACS Sept 1, but should have some decent time after
that.
Best,
Michael
On 8/11/05, gmx-developers-request at gromacs.org
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> Today's Topics:
>
> 1. Re: More about the Ekin issue. (Berk Hess)
> 2. Re: More about the Ekin issue. (Xavier Periole)
> 3. Re: More about the Ekin issue. (Berk Hess)
> 4. Re: More about the Ekin issue. (hessb at mpip-mainz.mpg.de)
> 5. Re: More about the Ekin issue. (David)
> 6. Re: More about the Ekin issue. (David)
> 7. Re: More about the Ekin issue. (hessb at mpip-mainz.mpg.de)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 11 Aug 2005 17:37:30 +0200
> From: Berk Hess <hessb at mpip-mainz.mpg.de>
> Subject: Re: [gmx-developers] More about the Ekin issue.
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <42FB70BA.6090804 at mpip-mainz.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> >>But do you also run the REMD in NpT?
> >>Then you have a pV term which you probably did not account for in the
> >>exchange.
> >>If you do account for the pV term it is around 10x as larger as the
> >>energy difference
> >>and will therefore ruin the efficiency (and maybe accuracy) of your REMD.
> >>
> >>
> >According to Xavier's mdp file he does use NPT simulation, the question
> >is which REMD he uses...
> >
> >I'm not sure whether including the pV term is bad, it make the
> >acceptance ratio go to 40%, but the overall number of exchanges also
> >depends on the frequency with which you try to exchange. The guys that
> >make all these algorithms don't usually test it on proteins, but on
> >simple model systems.
> >
> >
> The acceptance ratio does not say anything about efficiency.
> The pV term is roughly 10x larger the energy term, so the energy difference
> has a negligible influence on the exchange probability.
> The exchange probability is almost fully determined by pV.
> Fluctuations in the solvent probably contribute most to pV.
> So you just exchange based on fluctuations in the solvent
> and not on the conformation of the solute.
> I have no idea how efficient REMD based (mainly) on the pV criterion is.
>
> Another issue is that the pV distribution with Berendsen pressure
> coupling is quite off for small systems. For 400 waters:
> Berendsen: pV RMSD 375 kJ/mol
> Parrinello-Rahman: pV RMSD 490 kJ/mol
>
> Berk.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 11 Aug 2005 17:35:56 +0200
> From: Xavier Periole <x.periole at rug.nl>
> Subject: Re: [gmx-developers] More about the Ekin issue.
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <42FB705C.1060200 at rug.nl>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> David van der Spoel wrote:
>
> >>The energy difference is probably completely (except for the less than 1
> >>K Ekin effect)
> >>due to the reaction-field correction for excluded atom pairs.
> >>The term is written in the log and energy file and there is an option in
> >>the mdp
> >>file to use the old reaction-field. Using the old tpr will also cause
> >>3.3 to use the old RF.
> >>This term might be present in Gromos which explains the agreement.
> >>The term is a constant for rigid molecules and shows negligible fluctuations
> >>for flexible molecules. It will therefore not affect your replica exchange.
> >>
> >>But do you also run the REMD in NpT?
> >>Then you have a pV term which you probably did not account for in the
> >>exchange.
> >>If you do account for the pV term it is around 10x as larger as the
> >>energy difference
> >>and will therefore ruin the efficiency (and maybe accuracy) of your REMD.
> >>
> >>
> >According to Xavier's mdp file he does use NPT simulation, the question
> >is which REMD he uses...
> >
> >I'm not sure whether including the pV term is bad, it make the
> >acceptance ratio go to 40%, but the overall number of exchanges also
> >depends on the frequency with which you try to exchange. The guys that
> >make all these algorithms don't usually test it on proteins, but on
> >simple model systems.
> >
> >
> >
> Wait ... the REMD is in NVT. The mdp file is from a Brute Force MD
> simulations
> I produced to compare REMD to BFMD. BFMD are done both in NPT and NVT.
> The mdp I gave and used for the comparison are NPT simulation.
>
> I am making more test on the RF. Let you know
> XAvier
>
> --
> ----------------------------------
> Xavier Periole - Ph.D.
>
> Dept. of Biophysical Chemistry / MD Group
> Univ. of Groningen
> Nijenborgh 4
> 9747 AG Groningen
> The Netherlands
>
> Tel: +31-503634329
> Fax: +31-503634800
> email: x.periole at rug.nl
> web-page: http://md.chem.rug.nl/~periole
> ----------------------------------
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 11 Aug 2005 17:57:58 +0200
> From: Berk Hess <hessb at mpip-mainz.mpg.de>
> Subject: Re: [gmx-developers] More about the Ekin issue.
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <42FB7586.1050800 at mpip-mainz.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Berk Hess wrote:
>
> >
> >>> But do you also run the REMD in NpT?
> >>> Then you have a pV term which you probably did not account for in
> >>> the exchange.
> >>> If you do account for the pV term it is around 10x as larger as the
> >>> energy difference
> >>> and will therefore ruin the efficiency (and maybe accuracy) of your
> >>> REMD.
> >>>
> >>
> >> According to Xavier's mdp file he does use NPT simulation, the question
> >> is which REMD he uses...
> >> I'm not sure whether including the pV term is bad, it make the
> >> acceptance ratio go to 40%, but the overall number of exchanges also
> >> depends on the frequency with which you try to exchange. The guys that
> >> make all these algorithms don't usually test it on proteins, but on
> >> simple model systems.
> >>
> >>
> > The acceptance ratio does not say anything about efficiency.
> > The pV term is roughly 10x larger the energy term, so the energy
> > difference
> > has a negligible influence on the exchange probability.
> > The exchange probability is almost fully determined by pV.
> > Fluctuations in the solvent probably contribute most to pV.
> > So you just exchange based on fluctuations in the solvent
> > and not on the conformation of the solute.
> > I have no idea how efficient REMD based (mainly) on the pV criterion is.
> >
> > Another issue is that the pV distribution with Berendsen pressure
> > coupling is quite off for small systems. For 400 waters:
> > Berendsen: pV RMSD 375 kJ/mol
> > Parrinello-Rahman: pV RMSD 490 kJ/mol
> >
> Now I thought a bit more I think the huge fluctuations are the problem.
> The average pV for 400 waters should be around 12 kJ/mol.
> If there were no large fluctuations the exchange criterion would produce
> proper and efficient REMD sampling. An increased temperature might
> increase the average pV by 0.1 kJ/mol.
> But the enourmous fluctuations will dominate the exchanges and cause
> all exchanges to be random. If you attempt to exchange infrequently
> the normal MD sampling will correct a bit for this, but the ensembles
> will probably still be quite incorrect.
>
> (Note that a molecular virial will not help as there are no intramolecular
> interactions in water)
>
> Berk.
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 11 Aug 2005 18:50:13 +0200
> From: hessb at mpip-mainz.mpg.de
> Subject: Re: [gmx-developers] More about the Ekin issue.
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <1123779013.42fb81c57a9b9 at https.mpip-mainz.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I think the whole NPT REMD issue (which is no longer
> related to the subject) is caused by the, probably,
> incorrect CVS implementation of David.
>
> I think the highly fluctuating, meaningless instantaneous
> pressure in the criterion should be replaced by the reference
> pressure, as one considers an constant NPT ensemble.
> Just like a constant T is used in the criterion.
> The pV term then only depends on the instananeous volume,
> which fluctations do have meaning.
>
> BTW I think there is also a factor 1/PRESFAC missing in the exchange criterion.
>
> Then there is still the barostat issue.
> 400 waters at 300K, p=1 bar for 10 ns give:
> Berendsen volume: 11.968 rmsd 0.089
> Parrinello-Rahman: 11.977 rmsd 0.150
>
> Berk.
>
>
> -------------------------------------------------
> This mail sent through IMP: http://horde.org/imp/
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 11 Aug 2005 19:01:06 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-developers] More about the Ekin issue.
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <1123779666.4530.2.camel at localhost.localdomain>
> Content-Type: text/plain
>
>
> > > The acceptance ratio does not say anything about efficiency.
> > > The pV term is roughly 10x larger the energy term, so the energy
> > > difference
> > > has a negligible influence on the exchange probability.
> > > The exchange probability is almost fully determined by pV.
> > > Fluctuations in the solvent probably contribute most to pV.
> > > So you just exchange based on fluctuations in the solvent
> > > and not on the conformation of the solute.
> > > I have no idea how efficient REMD based (mainly) on the pV criterion is.
> > >
> > > Another issue is that the pV distribution with Berendsen pressure
> > > coupling is quite off for small systems. For 400 waters:
> > > Berendsen: pV RMSD 375 kJ/mol
> > > Parrinello-Rahman: pV RMSD 490 kJ/mol
> > >
> > Now I thought a bit more I think the huge fluctuations are the problem.
> > The average pV for 400 waters should be around 12 kJ/mol.
> Where do you get that number from?
>
> There definitely is no detectable correlation between protein structure
> and energy...
>
>
> > If there were no large fluctuations the exchange criterion would produce
> > proper and efficient REMD sampling. An increased temperature might
> > increase the average pV by 0.1 kJ/mol.
> > But the enourmous fluctuations will dominate the exchanges and cause
> > all exchanges to be random. If you attempt to exchange infrequently
> > the normal MD sampling will correct a bit for this, but the ensembles
> > will probably still be quite incorrect.
> >
> > (Note that a molecular virial will not help as there are no intramolecular
> > interactions in water)
> >
> > Berk.
> >
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-developers-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 11 Aug 2005 19:05:03 +0200
> From: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-developers] More about the Ekin issue.
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <1123779903.4530.4.camel at localhost.localdomain>
> Content-Type: text/plain
>
> On Thu, 2005-08-11 at 18:50 +0200, hessb at mpip-mainz.mpg.de wrote:
> > I think the whole NPT REMD issue (which is no longer
> > related to the subject) is caused by the, probably,
> > incorrect CVS implementation of David.
> >
> > I think the highly fluctuating, meaningless instantaneous
> > pressure in the criterion should be replaced by the reference
> > pressure, as one considers an constant NPT ensemble.
> > Just like a constant T is used in the criterion.
> > The pV term then only depends on the instananeous volume,
> > which fluctations do have meaning.
> >
> > BTW I think there is also a factor 1/PRESFAC missing in the exchange criterion.
> Any obvious bugs apart from that then?
>
> I will replace the instantaneous pressure by the constant trace of the
> reference pressure.
> >
> > Then there is still the barostat issue.
> > 400 waters at 300K, p=1 bar for 10 ns give:
> > Berendsen volume: 11.968 rmsd 0.089
> > Parrinello-Rahman: 11.977 rmsd 0.150
>
> This is not relevant but the derived volume fluctuations are of course.
>
> >
> > Berk.
> >
> >
> > -------------------------------------------------
> > This mail sent through IMP: http://horde.org/imp/
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-developers-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 11 Aug 2005 19:11:09 +0200
> From: hessb at mpip-mainz.mpg.de
> Subject: Re: [gmx-developers] More about the Ekin issue.
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <1123780269.42fb86ad3e20d at https.mpip-mainz.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Quoting David <spoel at xray.bmc.uu.se>:
>
> > On Thu, 2005-08-11 at 18:50 +0200, hessb at mpip-mainz.mpg.de wrote:
> > > I think the whole NPT REMD issue (which is no longer
> > > related to the subject) is caused by the, probably,
> > > incorrect CVS implementation of David.
> > >
> > > I think the highly fluctuating, meaningless instantaneous
> > > pressure in the criterion should be replaced by the reference
> > > pressure, as one considers an constant NPT ensemble.
> > > Just like a constant T is used in the criterion.
> > > The pV term then only depends on the instananeous volume,
> > > which fluctations do have meaning.
> > >
> > > BTW I think there is also a factor 1/PRESFAC missing in the exchange
> > criterion.
> > Any obvious bugs apart from that then?
> >
>
> I don't think so.
>
> > I will replace the instantaneous pressure by the constant trace of the
> > reference pressure.
>
> 1/3 of the trace I guess?
>
> > >
> > > Then there is still the barostat issue.
> > > 400 waters at 300K, p=1 bar for 10 ns give:
> > > Berendsen volume: 11.968 rmsd 0.089
> > > Parrinello-Rahman: 11.977 rmsd 0.150
> >
> > This is not relevant but the derived volume fluctuations are of course.
>
> What is not relevant?
> You mean the difference between the average volumes?
>
> For the fluctuations I am not sure what is correct.
> I hope the current Parrinello-Rahman implementation is correct,
> but I have not really used it myself.
>
> Can one analytically derive what the volume fluctuations should be?
>
> I was also wondering if a Langevin type of barostat exists.
>
> Berk.
>
>
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