[gmx-users] Questions about OPLS force fields

[Dan Gil]

Hi,

I am creating a topology for a molecule that is not defined by OPLS. I have
some questions that I want to ask:

1. What is bondtype and ptype in ffnonbonded.itp?

2. If I use the Buckingham potential to define nonbonded interactions
between atom A and atom B, does this potential apply to all A and B atoms
in the system? For example, I have a molecule that has oxygen atoms. I
define the Buckingham potential of oxygen atoms with various other atoms in
an .itp file of this molecule. If I have water molecules as the solvent,
how will the .itp file affect the interactions between water molecules?

2. When do I need [ pairs ] directive, and when do I not? If I use the
buckingham potential, do I not need it?

Best Regards,

Dan