[gmx-users] fluorine parameters in GROMACS

Makoto Yoneya yoneya at nanolc.jst.go.jp
Tue Mar 19 07:07:20 CET 2002

Dear GROMACS users:

I'm trying to run MD of fluorine containing molecule with GROMACS-3.0.5.
But, I'm confusing the difference of fluorine LJ (c6,c12) parameters between
GROMOS and related literature.

The standard GROMACS force fields (ffgmxnb.itp) lists as
[ atomtypes ]
      ;name        mass      charge   ptype            c6           c12
          F    18.99840       0.000       A   0.78301E-02   0.25209E-04,
and GROMOS (ffG43b1nb.itp) lists as
          F     0.000      0.000     A  0.0011778624  7.6073284e-07.
These c6 and c12 are largely different each other.
Some literatures from GROMACS group lists,
          F                                A   1.177862E-03   1.000000E-06
in Fioroni,M. et. al J.Phys.Chem,B'00 104, and
          F                                A   1.177862E-03   1.168000E-06
in Fioroni,M. et. al J.Phys.Chem,B'01 105.
These are close to that of GROMOS as the author says.
And fluorine parameters in CVFF force fields (e.g. Koike & Yoneya
J.C.P.,105,'96) are,
          F                                     0.9847354E-03
and again rather similar to GROMOS ones.
GROMACS manual says the F parameters are from van Buuren & Berendsen,
Biopolymers 33, '93.
In this literature, epsilon and sigma for fluorine was listed as 66.61K and
and these gives c6 and c12 as,
          F                                A   1.78334E-03   1.43560E-06.
These values are rather similar to GROMOS parameters not to GROMACS.
I'm wondering where are the GROMACS LJ parameters, i.e.,
          F    18.99840       0.000       A   0.78301E-02   0.25209E-04,
comes from and are these largely different valued parameters valid for
standard MD?
And when I want to use non-standard fluorine parameters with other GROMACS
where have to rewrite in force field files.

Please make happy who wants simulate fluorine containing molecule!
Thank you for advance.

Makoto Yoneya (Dr.)
ERATO Yokoyama Nano-structured Liquid Crystal Project

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