[gmx-users] Re: question about the Silicon force field in gromacs

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 13 11:59:05 CET 2010

On 1/13/10 11:48 AM, Baofu Qiao wrote:
> Dear prof. van der Spoel,
> I am planning to study the Silicon crystalline. But I have one question
> about the force field of silicon. In the original paper, (E. J. W.
> Wensink, et al., Properties of Adsorbed Water Layers and the Effect of
> Adsorbed Layers on Interparticle forces by Liquid Bridging,  Langmuir,
> 2000, 16, 7392-7400.), the LJ parameters are given as C6=0.22617*10^(-2)
> kJ nm^6/mol, and C12=0.22191*10^(-4) kJ nm^12/mol.
> While in ffG53a6nb.itp,  C6= 0.01473796, C12= 2.2193521e-05. The value
> of C6 is different, with the same value of C12. Is there an error in the
> inconsistence, or I missed something?
> PS: in ffoplsaanb.itp, sigma=3.38550e-01, epsilon= 2.44704e+00, which is
> consistent with the ffG53a6nb.itp.
> Since it is you who added the force field of silicon, and you have one
> related publication (D. van der Spoel, et al.,  Lifting a Wet Glass from
> a Table: A Microscopic Picture, Langmuir, 2006, 22, 5666.), I think you
> might be able to give me some help. Thanks a lot!
> best wishes,
> Baofu Qiao
In the latter paper we use OPLS. The parameter in there was copied from 
the GROMOS family of force fields. This C6 is also the one that is 
listed in the GROMOS96 manual. So it seems that the outlier is the 
Wensink2000 paper, since I was not part of that work I do not know where 
these parameters came from.

A relevant question would be how good the parameters are, and I can not 
answer that.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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