[gmx-users] Nonbond params and pairtypes section in ffnonbonded.itp

[Apramita Chand]

Dear All,
 I've asked in my previous posts about how to supply parameters in the
nonbond_params and pairtypes section of the ffnonbonded.itp, depending on
different combination rules. From the manual, it seems that nonbonded
parameters are calculated from the combination rules.
>From the recent reply by Dr.Lemkul, it appears that gromos uses a complex
matrix of combination rules for different parameters.Also, LJ parameters
cannot be calculated through any predicted equations

Now, my predicament is that I want to use a model for TMAO molecule, say
the Shea model in gromos 53a6ff. It uses the geometric combination of sigma
and epsilon for calculation of nonbonded parameters.
I have changed the atomtypes section to include sigma and epsilon values
and specified the combination rule as 3.
But what parameters should I supply to the nonbonded parameters and
pairtypes section??

Can I manually calculate the nonbonded parameters according to the
combination rule ( sigma(ij) and epsilon (ij)) and input them?

What about pairtypes section?
How are these values different from the nonbond params section? How should
I manually calculate them?


Please help as I am stuck with this problem.


Yours sincerely,
Apramita Chand