Lars,
I can't comment as to where the polarizability values come from (I'd wager
that they are from experiment), but I do know that they are not used in the
standard force fields and are not necessary entries in the leaprc/frcmod
files. The value given for sodium likely did not affect your simulations at
all.
Regards,
Brian
On Wed, Sep 25, 2013 at 12:27 AM, Lars Holte <larskholte.gmail.com> wrote:
> Hello,
>
> I am attempting to track down a literature citation for the sodium ion
> parameters used in my simulations. They come from the file
> frcmod.ionsjc_tip4pew. The title information in this file lists Joung &
> Cheatham JPCB (2008) as the primary source. I have identified that article
> as *J. Phys. Chem. B*, *112*, 9020-9041 (*2008*). The polarizability for
> sodium is listed as coming from a different source:
>
> Na+ 22.99 0.250 sodium pol: J. Phys. Chem.
> 11,1541,(1978)
>
> I cannot identify the article to which this reference refers. Volume 11 of
> the Journal of Physical Chemistry is from 1906, not 1978. There is an
> article which starts on p. 1541 of volume 82, published in 1978, but it
> deals with the complexation of the Nickel(II) cation with pyridine, and
> appears to have little to do with molecular dynamics.
>
> Thanks in advance,
> Lars Holte
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--
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Brian Radak : BioMaPS
Institute for Quantitative Biology
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Received on Wed Sep 25 2013 - 06:30:05 PDT
