[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.

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

More information about the gromacs.org_gmx-developers mailing list