How use desired mixing rule in gromacs?

User discussions
1

Dear Gromacs users:

As you know there are different combination rules in Gromacs for non bonded interactions. I would like to use different combination rules to see the results. How can I apply them into the MD calculations?

Thanks

2

Hi @mj.rezayani

You can change the combination rules in the force field definition. Here are the main rules you can have. Somewhere, in the files defining your force field, you will have something like this

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333

The 2 here is the combination rule, the number you want to modify.

3

Dear Obzehn,

Thank you very much for your reply.

What about

fudgeLJ   and  fudgeQQ

Do I have to change them too?

4

Those are force field dependent and are coefficients that tune the generation of pairs, if I am not mistaken. Here there is some more documentation. So it depends on if you are generating pairs or not.

On a side note, if you are using an already established force field, I wouldn’t touch any numbers in that [ default ] section as you will most likely change completely the behaviour intended by the developers of the ff. Also, nbfunc = 2 (that is Buckingham potential) has been deprecated since 2019 I think, so it wont work in case you need it.

5

Thanks for your reply,

Actually, I am using the parameters from the paper and it is not based on a specific forcefield and I have to manually define the parameters and settings.

That’s why I am asking about the options.

Thanks again