[gmx-users] manually adding non-bonded interactions based on atom number to topology file

[Amanda Parker]

​Hello,

I am trying to create my own topology file in order to simulate assembly of
a number of identical monomers. I have been reading the manual, mailing
list, and other online sources, about what all the sections in the topology
mean and how to construct them, but I'm still confused about what is
necessary and what overrides what.

I would like to be able to have any number of monomers in my system and
therefore I want all the intermolecular interactions to be non-specific. I
want each monomer to have atom numbers running from 1 to last_atom_number,
so that I can have atom 1 paired with atom last_atom_number, and see
binding between any monomer's atom 1 with any other monomer's atom
last_atom_number.

So my idea is to create a single topology file, which will contain the
intramolecular interactions for a single monomer, as well as the
interactions between atom 1 and atom last_atom_number. The latter will
probably be Lennard-Jones interactions, since that way the "beginning" of
one monomer will not interact with its own "end" (due to the cut-off), but
with other monomers' ends if they get close enough. I'd like to manually
adjust the parameters for these interactions, to accelerate binding.

The problem is that I don't know where to put these Lennard Jones
interactions.

Right now I have them in the [ pairs ] section, since my understanding is
that this is where one can put "extra" non-bonded interactions with special
parameters. But it also seems like this depends on the force field and that
sometimes [ pairs ] should only be for a list of 1-4 interactions. Since
I'm writing my own topology (not using pdb2gmx), what will [ pairs ]
specify? Will the parameters in [ pairs ] override the parameters in [
atomtypes ]? I have increased the c6 parameter and decreased the c12
parameter considerably, and I'm still not seeing any sign of attraction
between monomer-monomer interfaces.

[ nonbonded_params ] actually seems like the right place, since I've read
that the parameters there *will* override the combination rules, but it
looks like this section doesn't take atom numbers, but only atom types.
Since I want these bonds to be based on site locations, this won't work. Is
there a way to specify non-bonded parameters using atom numbers?

Any clarification you can provide will be helpful.

Thanks,​
Amanda