[gmx-users] Question regarding nrexcl and gen-pairs for angle terms with incomplete bonds (ClayFF)

[Thomas Underwood]

Dear GMX'ers,

I have a brief question regarding the use of nrexcl and gen-pairs when used with a non-bonded forcefield, such as ClayFF. I've had a brief look through previous posts but haven't found a completely satisfactory answer.

Currently, I have a system that is entirely non-bonded. The exception to this is hydroxyl groups.
In addition, there is an angle term between the hydroxyl group and an adjacent metal atom.
I'm wondering what implications this angle term has on the nonbonded interactions of my system.

Let's say I have a triplet of atoms: {i,j,k}.
I define a bond between atoms i and j; I have an angle defined between i, j, and k; but I have NO angle defined between j and k.

Now, if I set nrexcl = 1, will the nonbonded interaction between j and k still be present in my simulation? I.e. does the angle term at all affect the outcome of my pair interactions?

Overall, I need nonbonded interactions between atoms {i,k} and {j,k} in this setup.

Further, gen-pairs is typically used for 1-4 interactions. However, when I set nrexcl less than 3, does this also generate 1-3 interactions, such as the one between i and k above?

Thanks in advance,

Tom