[gmx-users] Gromos parameters for atom type OA

[Patrick Fuchs]

Hi,
slightly off-thread, I'd like to add that the oxygen parameters of 53a6 
have been recently refined in a new set called 53a6OXY 
(http://pubs.acs.org/doi/abs/10.1021/ct1006407). So this ends up in new 
values for LJ and charges for the OA atom (as well as for other oxygen 
atoms).
Cheers,

Patrick

Le 09/12/2011 20:03, Javier Cerezo a écrit :
> 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
>
>
>

-- 
_______________________________________________________________________
Patrick FUCHS
Dynamique des Structures et Interactions des Macromolécules Biologiques
INTS, INSERM UMR-S665, Université Paris Diderot,
6 rue Alexandre Cabanel, 75015 Paris
Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19
E-mail address: patrick.fuchs at univ-paris-diderot.fr
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