GROMOS force field builds the LJ parameters by multiplication of the
square-rooted parameters per atom type (hence the SQRT(C6) and SQRT(C12)
labels). In the case of the repulsion term (C12), up to three of such
parameters are possible: SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)), when
combined with other atoms, depending on the desired repulsion strength
(e.g. the enhanced C12(3) repulsion is used to keep charged groups
separated). Which of the three is used depends on the combination of
atoms, and is specified in an (asymmetric) matrix (see pages 14 and 15
in the pdf pages of 45a3 and 54a6 force fields from the GROMOS site, or
in the ifp file the last lines for each atom type containing "1", "2"
and "3"). For the case of OA, this matrix specifies that the second C12
term is to be used when OA encountes another OA. So, according, to the
ifp line you showed:
C12(OA-OA) = SQRT(C12(2))_OA * SQRT(C12(2))_OA = 1.227E-3 * 1.227E-3 =
1.50553E-6
Which is the same for 45a3 and 54a6 force fields.
Differences in the parameters will show up only in the cases where the
SQRT(C12(1)) term for OA is to be used (e.g C12(OA-CH2))
Javier
El 09/12/11 16:12, Samuli Ollila escribió:
Dear all,
I was comparing Gromos 45a3 and 53a6 force fields and I found
something which I cannot understand. The atom type OA is described in
ffG45a3nb.itp as:
;name at.num mass charge ptype c6 c12
OA 8 0.000 0.000 A 0.0022619536 1.505529e-06
and in ffG53a6nb.itp:
OA 8 0.000 0.000 A 0.0022619536 1.505529e-06
which are same parameters.
However, according to Gromos developers the atom type OA has been
changed between Gromos 45a3 and 53a6. The parameters given by Gromos
developers for 45a3 are
# IAC TYPE SQRT(C6) SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3))
3 OA 0.04756 1.1250E-3 1.227E-3 0.0
and for 53a6
3 OA 0.04756 1.100E-3 1.227E-3 0.0
The actual numbers are different for parameters used in Gromacs since
the way to write parameters is different.
My problem is that there is difference in OA type between 45a3 and
53a6 in parameters given by Gromos developers but not in the files
distributed in Gromacs package. Can someone explain this?
BR,
Samuli Ollila
--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434
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