Lars,
That is fine. If you are running with any off the standard force fields
(ff94, ff99SB, ff10, etc.), then the resulting prmtop files have NO
dependence on the values of polarizability. You could have put any number
in that field or even left it blank and the results would have come out
exactly the same. Therefore, I would argue, no such citation is necessary.
Brian
On Wed, Sep 25, 2013 at 1:26 PM, Lars Holte <larskholte.gmail.com> wrote:
> Hi Brian,
>
> Thanks for your response.
>
> I explicitly imported the parameters from frcmod.ionsjc_tip4pew in my leap
> script, so I know that they are being used. Unfortunately, I did not take
> the time to investigate this reference when I started the simulations, and
> it is only now that I realize I cannot give a citation for the sodium ion
> polarizability.
>
> Lars
>
>
> On Wed, Sep 25, 2013 at 6:08 AM, Brian Radak <radak004.umn.edu> wrote:
>
> > 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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> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
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> appropriate
> > address.
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Wed Sep 25 2013 - 12:30:02 PDT
