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

Wes Barnett w.barnett at columbia.edu
Thu Sep 28 03:07:16 CEST 2017

On Wed, Sep 27, 2017 at 8:07 PM, Amanda Parker <asparker at ucdavis.edu> wrote:

> ​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.

Before delving into this too much, to clarify: you want to simulate a
polymer melt with some modified interactions between the ends of each

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu

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