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

Michael R Shirts Michael.Shirts at Colorado.EDU
Wed May 24 21:45:34 CEST 2017

Although the numbers I list are still different from the ones that were suggested then (though those match pretty well with the tleap numbers).

Michael Shirts
Associate Professor
michael.shirts at colorado.edu
Phone: (303) 735-7860
Office: JSCBB C123
Department of Chemical and Biological Engineering
University of Colorado Boulder

On 5/24/17, 1:18 PM, "gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Igor Leontyev" <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of ileontyev at ucdavis.edu> wrote:

    Hi all. The issue was discussed in past but nothing was corrected since 
    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
    >  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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