[gmx-users] Re: bug in ffoplsaanb.itp?
dmobley at gmail.com
Sun Apr 1 05:00:23 CEST 2007
Thanks. That's very helpful. I'm actually not using OPLS at all myself
-- I just stumbled across this really odd looking set of F- parameters
when troubleshooting for someone else. Anyway, your comments are very
helpful. I appreciate it.
On 3/31/07, Alan Chen <achen at artsci.wustl.edu> wrote:
> I would be extra cautious before using any of the early OPLS ion parameters
> which are derived
> from really early Hartree-Fock calculations. Note that in standard OPLS
> usage many of the aforementioned
> parameters are superceded by OPLS types 406-410 which are aqvist-derived
> (and therefore are almost
> identical to the aqvist-derived AMBER ions except for the differing
> combination rule).
> If you check out the 1984 OPLS paper you will also notice that these
> parameters are meant only to be
> used with TIP4P (to get the right free energy of solvation), while aqvist
> is meant to be used with TIP3P/SPC.
> I've been doing similar literature digging, and I suspect the reason there
> was early consensus on Cl- is simply
> because there was lots of scattering data available at that time of aqueous
> chloride salts but none on fluoride salts:
> the location of the first ion-water oxygen peak in the RDF seems to be the
> primary sanity check that a reasonable size
> was chosen. Without a size constraint, you can imagine getting the "right"
> free energy of hydration with many
> degenerate pairs of sigma and epsilon.
> Lastly, I'll mention that the extra-deep OPLS F- potential leads to really
> screwy behavior - if you run a 100 mm box of NaF
> in tip3p water (298K 1Atm) you'll find almost all of them form really,
> really long lived contact ion pairs (half-life > 10ns).
> This is a full two orders of magnitude longer than the the transient and
> relatively rare NaCl pairs (aqvist) you
> would find at the same concentration . . .
> Alan Chen
> Graduate Student
> Pappu Lab
> Washington University in St. Louis
> Erik and all,
> > No, I don't think so, or at least it's not our typo :-)
> > It is quite common that ions end up with strange radii when you
> > parametrize for free energy of solvation, and in addition those
> > parameters are somewhat old (1984). Here's the extract from Bill
> > Jorgensens file that we translated them automatically from:
> > 400 09 F- -1.0
> 2.73295 0.72000 F- JACS 106, 903 (1984)
> > 401 17 ?? -1.0
> 4.41724 0.11779 Cl- JACS 106, 903 (1984)
> > 402 35 ?? -1.0
> 4.62376 0.09000 Br- JACS 107, 7793(1985)
> > 404 03 Li 1.0
> 1.25992 6.25000 Li+ JACS 106, 903 (1984)
> > 405 11 Na 1.0
> 1.89744 1.60714 Na+ JACS 106, 903 (1984)
> OK, that is weird. If I plot the Cl potential energies from AMBER and
> OPLS, they are almost identical. But if I plot F from OPLS versus F
> from AMBER, the well is roughly, well, 10x as deep in OPLS as AMBER...
> I guess you're off the hook in terms of it being your typo... But I'm
> still not convinced it's right. Ugh. My understanding is that the LJ
> parameters from AMBER and OPLS have roughly similar origins, so it
> doesn't make a lot of sense to me to just say that AMBER is wrong --
> especially when Cl and the other ion parameters are pretty consistent.
> I suppose I will have to dig into the literature. Anyway, thanks for
> the response.
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