[gmx-developers] high-precision TIP3P parameters?
Mark Abraham
mark.j.abraham at gmail.com
Sat May 27 10:47:57 CEST 2017
On Sat, May 27, 2017 at 10:17 AM Igor Leontyev <ileontyev at ucdavis.edu>
wrote:
> Hi,
> It is unlikely that inaccuracy in 4th digit of the parameters could
> introduce significant error in simulation results.
>
> However, for the energy comparison and debugging which is often made by
> curious people (including myself) when switching between Amber and
> Gromacs codes the inaccuracy is really bothering. Accepting suggested
> correction will match Amber and Gromacs code energies and make the
> comparison perfect (possibly for the cost of one time issue with
> regression test).
>
True, but also makes GROMACS different from past versions of itself, which
also would worry people doing such a comparison when e.g. contemplating
upgrading their version. We're all for doing things correctly, but that
should mean everybody actually implementing the published/accepted value,
not agreeing with each other on how to be different.
It sounds like we're happy enough to change the values in GROMACS to match
the paper - can people please raise the issue/question with others who
distribute parameter sets?
Mark
> Igor
>
> >
> > Hi,
> >
> > These difference are irrelevant for any practical purposes, since the
> > model (and sampling) is not by far that accurate. But it would still be
> > nice to have all decimals that we have in files correct.
> > Is this somehow related to the differences in the kcal/mol to kJ/mol
> > conversion in different packages and/or at different times?
> >
> > Cheers,
> >
> > Berk
> >
> > On 24/05/17 21:18 , Igor Leontyev wrote:
> >> Hi all. The issue was discussed in past but nothing was corrected
> >> since then.
> >>
> >>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2011-April/005178.html
> >>
> >>
> >> To make gromacs TIP3P energies matching Amber code energies:
> >>> Suggested correction in amberXX.ff/ffnonbonded.itp:
> >>> ;OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01
> >>> OW 8 16.00 0.0000 A 3.15076e-01 6.35968e-01
> >>
> >> Igor
> >>
> >>> So, going back to the original TIP3P paper, the parameters are listed
> >> as A and C parameters (in the formula a/r^12 ? b/r^6).
> >>>
> >>> The parameters listed there are A = 582000 A^12 kcal/mol and C = 595
> >>> A^6 kcal/mol.
> >>>
> >>> Converting to sigma/epsilon form, this gives:
> >>> Sigma = 0.31506561105 nm
> >>> Epsilon = 0.6362717354 kJ/mol
> >>>
> >>> This compares with the values in the most of the distributed ITP
> >>> files of
> >>>
> >>> Sigma = 0.315061 nm (a difference of 4.6 x 10^-6 nm, or a relative
> >>> difference of of 1.4 x 10^-5)
> >>> Epsilon = 0.636386 kJ/mol (a difference of 1.1 x 10^4 kJ/mol, or a
> >>> relative difference of 1.8 x 10^-4)
> >>> (note the GROMACS one is also 0.152100
> kcal/mol)
> >>> I don?t know how much of a difference this would make (likely a
> >>> difference of the scale of).
> >>>
> >>> Now, that?s in the original paper. What values are ACTUALLY
> >>> specified by other codes?
> >>>
> >>> For AMBER, (as produced by tleap), it outputs.
> >>>
> >>> A = 581935.564 A^12 kcal/mol
> >>> C = 594.825035 A^6 kcal/mol
> >>>
> >>> Which leads to:
> >>>
> >>> Sigma = 0.315075 (a difference of 3.0 x 10^-5 nm, or a relative
> >>> difference of 3.0 x 10^-5)
> >>> Epsilon = 0.635968 kJ/mol (a difference of 9.4 x 10^4 kJ/mol or a
> >>> relative difference of 4.7 x 10^-4)
> >>> (which is also 0.152000 kcal/mol)
> >>>
> >>> So ? I don?t know. Nobody seems to be getting it _exactly_ right,
> >>> and it?s also not so clear how much of a difference it makes. One
> >>> can estimate that enthalpies would have a relative error of around
> >>> 10^-4, and relative errors in the density of 3*dsigma = 10^-4 to 10^-5.
> >>>
> >>> So I don?t know that there is anything actionable to take. Just
> >>> thought it was interesting to bring out. Something to ponder for now.
> >>
>
> >
> > I?d say ?probably? irrelevant for practical purposes. It wouldn?t take
> too much simulation time to determine the density sensitively enough to
> tell the difference. But, pretty much irrelevant.
> >
> > ? Is this somehow related to the differences in the kcal/mol to
> kJ/mol
> > ? conversion in different packages and/or at different times?
> >
> > I think that it?s due to differences in rounding from the original A and
> C values vs. rounding from conversion of them to epsilon and sigma values.
> The epsilons in AMBER and GROMACS are clearly equal to using either
> 0.152100 or 0.15200 kcal/mol as the value (the parameters in the original
> paper correspond to 0.151207).
> >
> > I think there might have been a kJ/kcal issue at some point, but those
> were fixed a decade or so ago (I seem to recall that popping up when I was
> a graduate student, but not since then).
> >
> > ? These difference are irrelevant for any practical purposes, since
> the
> > ? model (and sampling) is not by far that accurate. But it would
> still be
> > ? nice to have all decimals that we have in files correct.
> >
> > At this stage, it probably involves getting some general set everyone
> together and deciding in what the ?right? values are. I could potentially
> do that . . . but as Berk points out, not that big a deal. Unless one is
> trying to match energy snapshots, and getting frustrated.
> >
> > For what it?s worth, the Desmond viparr utility uses for TIP3P:
> {"sigma": 3.15061, "epsilon": 0.1521}. Both match GROMACS .itp libraries,
> but not tleap or the original paper.
> >
> > Best,
> > ~~~~~~~~~~~~~~~~
> > Michael Shirts
> > Associate Professor
> > michael.shirts at colorado.edu
> > http://www.colorado.edu/lab/shirtsgroup/
> > Phone: (303) 735-7860
> > Office: JSCBB C123
> > Department of Chemical and Biological Engineering
> > University of Colorado Boulder
> >
> > On 5/25/17, 1:51 PM, "
> gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Berk
> Hess" <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf
> of hess at kth.se> wrote:
> >
> > Hi,
> >
> > These difference are irrelevant for any practical purposes, since the
> > model (and sampling) is not by far that accurate. But it would still
> be
> > nice to have all decimals that we have in files correct.
> > Is this somehow related to the differences in the kcal/mol to kJ/mol
> > conversion in different packages and/or at different times?
> >
> > Cheers,
> >
> > Berk
> >
> > On 24/05/17 21:18 , Igor Leontyev wrote:
> > > Hi all. The issue was discussed in past but nothing was corrected
> > > since then.
> > >
> > >
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2011-April/005178.html
> > >
> > >
> > > To make gromacs TIP3P energies matching Amber code energies:
> > > > Suggested correction in amberXX.ff/ffnonbonded.itp:
> > > > ;OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01
> > > > OW 8 16.00 0.0000 A 3.15076e-01 6.35968e-01
> > >
> > > Igor
> > >
> > >> So, going back to the original TIP3P paper, the parameters are
> listed
> > > as A and C parameters (in the formula a/r^12 ? b/r^6).
> > >>
> > >> The parameters listed there are A = 582000 A^12 kcal/mol and C =
> 595
> > >> A^6 kcal/mol.
> > >>
> > >> Converting to sigma/epsilon form, this gives:
> > >> Sigma = 0.31506561105 nm
> > >> Epsilon = 0.6362717354 kJ/mol
> > >>
> > >> This compares with the values in the most of the distributed ITP
> > >> files of
> > >>
> > >> Sigma = 0.315061 nm (a difference of 4.6 x 10^-6 nm, or a relative
> > >> difference of of 1.4 x 10^-5)
> > >> Epsilon = 0.636386 kJ/mol (a difference of 1.1 x 10^4 kJ/mol, or
> a
> > >> relative difference of 1.8 x 10^-4)
> > >> (note the GROMACS one is also 0.152100
> kcal/mol)
> > >> I don?t know how much of a difference this would make (likely a
> > >> difference of the scale of).
> > >>
> > >> Now, that?s in the original paper. What values are ACTUALLY
> > >> specified by other codes?
> > >>
> > >> For AMBER, (as produced by tleap), it outputs.
> > >>
> > >> A = 581935.564 A^12 kcal/mol
> > >> C = 594.825035 A^6 kcal/mol
> > >>
> > >> Which leads to:
> > >>
> > >> Sigma = 0.315075 (a difference of 3.0 x 10^-5 nm, or a relative
> > >> difference of 3.0 x 10^-5)
> > >> Epsilon = 0.635968 kJ/mol (a difference of 9.4 x 10^4 kJ/mol or a
> > >> relative difference of 4.7 x 10^-4)
> > >> (which is also 0.152000 kcal/mol)
> > >>
> > >> So ? I don?t know. Nobody seems to be getting it _exactly_ right,
> > >> and it?s also not so clear how much of a difference it makes.
> One
> > >> can estimate that enthalpies would have a relative error of around
> > >> 10^-4, and relative errors in the density of 3*dsigma = 10^-4 to
> 10^-5.
> > >>
> > >> So I don?t know that there is anything actionable to take. Just
> > >> thought it was interesting to bring out. Something to ponder for
> now.
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20170527/fc8a78ad/attachment-0003.html>
More information about the gromacs.org_gmx-developers
mailing list