[gmx-users] False C6/C12 parameter for DMSO and chloroform in GROMOS 45a3 force field (ffG45a3)
r.affentranger at gmail.com
Mon Jul 6 17:52:22 CEST 2009
I can not quite follow your arguments.
The original publication on the GROMOS96 43a1 force field (W.F. van
Gunsteren et al., "Biomolecular Simulation: The GROMOS96 manual and user
guide", Hochschulverlag AG an der ETH Zürich, 1996, Zürich, Switzerland)
explicitly gives the pair parameters for interactions between non-equal atom
types of DMSO (and of chloroform). See table 18.104.22.168.6 of the mentioned
ffG43a1nb.itp actually contains these values.
ffG45a3nb.itp contains the pair parameter one would obtain from the atomic
parameters using eq. 5.3 in the GROMACS 4.0 manual.
So the question is not so much which one is the right combination rule,
since the pair parameter are given explicitly in the original reference of
the GROMOS96 43a1 force field, and the values of DMSO (and chloroform) have
not been reparametrized for the 45a3 force field.
On Mon, Jul 6, 2009 at 5:07 PM, Markus Tusch <mtusch at mail.upb.de> wrote:
> Roman Affentranger schrieb:
>> Dear gmx-users (and developers ;-)
>> I believe there are false LJ pair-parameters in gromacs' implementation of
>> the GROMOS 45a3 force field for interactions between the atoms of DMSO,
>> between the atoms of chloroform. The C6/C12 pair paramteters for
>> CDMSO-SDMSO, ODMSO-SDMSO, ODMSO-CDMSO, and CLCHL-CCHL, HCHL-CCHL,
>> in ffG45a3nb.itp are simply the (root of the) product of the individual
>> atomic parameters, whereas separate parameters - with no relation to the
>> atomic ones - are defined in the original GROMOS force field.
> Hi Roman,
> I think there actually is a relation of the pair parameters to the
> individual atomic parameters in G43a1 as well as in G45a3 since all of the
> values are based on the same epsilon and sigma numbers.
> (For DMSO:
> epsilon = 1.297 kJ/mol for S, 1.7154 for O, 0.9414 for CH3
> sigma = 0.356 nm for S, 0.263 for O, 0.366 for CH3)
> The difference in the C6/C12 pair parameters apparently is due to the use
> of different combination rules (see GROMACSmanual-4.0.pdf, chapter 5.3.3).
> For G45a3 equations (5.1) and (5.3) are used to calculate the respective
> pair parameters, whereas for G43a1 eq. (5.4) and after that (5.1) are used.
> So I guess the question is, which is the right way for the combination?
>> The errors are
>> there in the force field files distributed with gromacs version 4.0.5 all
>> the way down to at least version 3.2.1 (it's as far as I've looked), and
>> also in the ffG45a3.tar.gz file to be found at
>> For example:
>> The lines in ffG45a3nb.itp read:
>> CDMSO SDMSO 1 0.009777435 2.1627421e-05
>> ODMSO SDMSO 1 0.004897196 4.0192831e-06
>> ODMSO CDMSO 1 0.0045335636 4.0434685e-06
>> However, they should be
>> CDMSO SDMSO 1 0.0097827 2.16523e-05
>> ODMSO SDMSO 1 0.0052442 4.6094e-06
>> ODMSO CDMSO 1 0.0049187 4.7597e-06
>> as they are in the GROMOS 43a1 force field.
>> A similar problem holds for chloroform (atoms CCHL, CLCHL and HCHL).
>> Find attached a corrected version of ffG45a3nb.itp.
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