[gmx-developers] gromacs.org_gmx-developers Digest, Vol 157, Issue 18
hess at kth.se
Thu May 25 21:51:41 CEST 2017
These difference are irrelevant for any practical purposes, since the
model (and sampling) is not by far that accurate. But it would still be
nice to have all decimals that we have in files correct.
Is this somehow related to the differences in the kcal/mol to kJ/mol
conversion in different packages and/or at different times?
On 24/05/17 21:18 , Igor Leontyev wrote:
> Hi all. The issue was discussed in past but nothing was corrected
> since then.
> 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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