Custom pair reactions

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1

GROMACS version:2021
GROMACS modification: No
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Hi Gromacs users,

I defined the top file to include oplsaa force field and clayff force field. Then I need to define a pair reaction between an atom from clayff force field and an atom from oplsaa force field. Their pair reaction does not follow the common mixing rule.
Is there any method to achieve this customed pair reaction?

Kind Regards,
Michel

2

This is done via the [nonbond_params] directive. You can supply any pre-computed values for the LJ terms here.

3

Thanks for your kind help, Dr Jalemkul.
May I ask if the definition is achieved in the .top file? If it is defined in the .top file, the atom types in the external force field need to be copied from their original defination to the .top file. Is it correct?

Kind Regards,
Michel

4

[nonbond_params] is a force-field level directive, not a molecule-level directive. It has to be defined before any [moleculetype] is introduced. See Chapter 5 of the manual for topology organization and more information on nonbonded settings. You don’t need to copy anything; you just need to add specific parameters in the appropriate sequence.

5

Many thanks, Dr Jalemkul. I’ll follow your guidance and try to sort it out.

Best Wishes,
Michel

6

Note that in practice with hydrated clays, zeolites, and similar materials if you are using SPC or SPC/E water, you do not need any [ nonbonded_params ] section to combine Clayff with OPLS/aa, since the Clayff oxygen atomtypes totally dominate the LJ energies (over the metal atomtypes contribution to the LJ energies), and since they have the exact same LJ parameters as oxygen (OW) in SPC / SPC/E water models. Hence the choice of mixing rule used with Clayff is not that important, as long it is used with SPC / SPC/E…
Best,
Michael Holmboe