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

Amanda Parker asparker at ucdavis.edu
Thu Sep 28 19:10:25 CEST 2017

Hi again,

For some reason I'm not getting your replies to my inbox, but I saw them in
the Digest.

Wes-- I would like to see a sort of phase transition, yes, in which a
number of monomers go from a disordered to ordered state. The ordered state
will look something like AB-AB-AB-... where AB represents a monomer that
has an A end and a B end (using Yu's description) that are identical, and
the "-" indicates an attractive interaction.

Yu-- Good point about the cut-off. Maybe you're right and I don't want
Lennard Jones for this. Also, can you tell me more about PLUMED?

Perhaps I made my question too convoluted. What I really want to know is
how to manually add interactions between particular atom numbers of a
single monomer. (The only caveat to this that might be important is that
I'll want these interactions to end up applying to a number of monomers
that will start far apart from each other.) Should I put them in [ pairs ],
[ nonbonded_params ], or elsewhere? What happens to the parameters
specified in [ atomtypes ] in each case? I'm worried that I'm changing the
parameters in [ pairs ], while gromacs is never actually using those
parameters, since maybe it thinks those should be 1-4 interactions (which
they're not) or because it's using different sets of parameters instead or
for some other reason.

Thanks again,


> ​Hello,
> I am trying to create my own topology file in order to simulate assembly
> a number of identical monomers. I have been reading the manual, mailing
> list, and other online sources, about what all the sections in the
> 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
> parameters. But it also seems like this depends on the force field and
> 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.
> 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



First, You must need a very long simulation box because one monomer's
length exceed the cut-off.

I don't think only LJ can naturely make monomers linear polymer. I know you
need acceleration of one monomer's A end binding to the other's B end. So I
will recommend the PLUMED to add some far-large-near-small restraints
between A and B end of different monomers.


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