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

[Igor Leontyev]

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.