[gmx-developers] gromacs.org_gmx-developers Digest, Vol 157, Issue 18

[Michael R Shirts]

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.
    >
    
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