[gmx-users] Questions about OPLS force fields

[Mark Abraham]

Hi,

On Thu, Jul 14, 2016 at 10:24 PM Dan Gil <dgilgmx at gmail.com> wrote:

> 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?
>

See chapter 5 of the manual for all these explanations.

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?


You don't specify non-bonded interactions between atoms, you specify
parameters for any such interactions, and they only happen if they're
inside the cutoff. Your big problem is deciding how to model the
interactions between atom types in your Buckingham molrecule with the atom
types in OPLS/AA in a way that makes any sense. I would strongly suggest
you get some GROMACS/MD experience with a normal simulation before
considering such questions.


> 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?
>

Depends on the atom type.


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

You need it when it helps you implement your intended model physics. It
does what it says in the manual ;-)

Mark


> Best Regards,
>
> Dan
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