[gmx-developers] high-precision TIP3P parameters?
Michael R Shirts
Michael.Shirts at Colorado.EDU
Wed May 24 01:20:40 CEST 2017
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.
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
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