[gmx-users] Intermolecular Nonbonded Interactions

[Justin Lemkul]

On 10/21/19 8:04 AM, Batuhan Kav wrote:
> Dear Al
>
> lI have a question regarding the non-bonded LJ interactions between two molecules. In particular about how Gromacs generates the non bonded LJ interactions between the water and protein molecules.
>
> In my system I am using a custom forcefield for the water molecules and Charmm36 for the protein. My intention is to change the epsilon/sigma LJ parameters between the water atoms and the protein atoms.
>
> For the sake of a simple test I use spc water model (spc.itp) to solvate the protein. As far as I can see in the ffnonbonded.itp there is the correct atom type for the spc water (in the [ atomtypes ] directive) defined however it lacks the protein-water atom pairs in the [ pairtypes ] section. This makes me think that when I run grompp it will generate the non bonded LJ interaction values between the protein and water atoms following the combination rule in the forcefield.itp file provided gen-pairs is set to “yes”. When I set gen-pairs to “no” I expected that grompp will complain that the LJ pairs for the water atom and protein atoms are missing. However grompp runs without any warnings/errors and the simulation can be started.
>
> Therefore my question is: how does Gromacs generate nonbonded interaction between the molecules if no specific atom-atom pairs are provided in the [pairtypes] and gen-pairs is “no”  (these atom-atom pairs are not defined anywhere in any part of the forcefield at all)?

Pairs refer specifically to intramolecular 1-4 interactions, so they are 
irrelevant for what you're trying to. Some force fields have special 
rules about whether or not special parameters are generated in these 
cases or omitted entirely if not listed in [pairtypes]. What you want to 
do is implement an NBFIX via the [nonbond_params] directive, which we 
list as a separate nbfix.itp file in the C36 port for GROMACS.

-Justin

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Justin A. Lemkul, Ph.D.
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