[gmx-users] Re: Re: Ion parameters in OPLS AA force field

[Dommert Florian]

On Wed, 2012-03-21 at 09:13 +0100, Kathleen Kirchner wrote: 
> Hello Florian,
> 
> I remembered a discussion with the same problem considering parameters 
> of Mg2+, here is the link:
> 
> http://comments.gmane.org/gmane.science.biology.gromacs.user/45437
> 
> The file given here
> 
> http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
> 
> mentions as source of the force field data
> 
> "OPLS All-Atom Parameters for Organic Molecules,
> Ions, Peptides&  Nucleic Acids, July 2008" as provided
> by W. L. Jorgensen, Yale University during June 2009
> 
> 
> and consists of a line
> 
> atom        641   86    La    "Lanthanum Ion La+3"          57   138.906    0
> 
> 
> Probably you can continue your research here.
> 
> Best regards and good luck
> Kathleen
> 
> 

Hello,

thank you very much. I also stumbled across the publication of Jorgensen
of 2009, but it seems to be a book, which is not accessible to me,
unfortunately.

However thank all of you very very much for the input.

Cheers,
Flo



> On 03/21/2012 05:55 AM, gmx-users-request at gromacs.org wrote:
> >> Hi Florian,
> >> >  
> >> >  I believe the ion parameters are the Aaqvist parameters:
> >> >  ie
> >> >  http://pubs.acs.org/doi/abs/10.1021/j100384a009
> >> >  
> >> >  Cheers
> >> >  
> >> >  Tom
> > Thank you very much for this first important hint. Unfortunately, there
> > parameters of for example La3+, given in GROMACS, are not provided
> > unfortunately.
> >
> > /Flo
> >
> >> >  
> >> >  Dommert Florian wrote:
> >>> >  >  Hello,
> >>> >  >  
> >>> >  >  there are several ion non-bonded ion parameters provided in the OPLS-AA
> >>> >  >  files of Gromacs, and the reference from an article Jorgensen et al.
> >>> >  >  from 2001. However I was not able to find the corresponding atom types
> >>> >  >  in this article and so far also not in any other article of the OPLS-AA
> >>> >  >  authors. Does anyone have an idea where these parameters come from ?
> >>> >  >  
> >>> >  >  /Flo
> >>> >  >  
> >>> >  >  
> >> >  
> >> >  -- 
> >> >  Dr Thomas Piggot
> >> >  University of Southampton, UK.
> 
> -- 
> Kathleen Kirchner
> PhD student
> Max Planck Institute for Mathematics in the Sciences
> (MPI f. Mathematik in den Naturwissenschaften)
> Inselstr. 22-26, D04103 Leipzig
> e-mail: kirchner at mis.mpg.de
> web: http://www.mis.mpg.de/scicomp/CompPhysChem/
> Tel +49 341 9959 725
> Fax +49 341 9959 999
> 

-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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