Alan,
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.
David
On 3/31/07, Alan Chen <[EMAIL PROTECTED]> 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parameters are superceded by OPLS types 406-410 which are aqvist-derived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 . . .
Cheers!
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.
David
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