[gmx-developers] high-precision TIP3P parameters?
ileontyev at ucdavis.edu
Thu May 25 02:47:14 CEST 2017
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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