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

Wes Barnett w.barnett at columbia.edu
Thu Sep 28 21:12:34 CEST 2017

On Thu, Sep 28, 2017 at 1:10 PM, Amanda Parker <asparker at ucdavis.edu> wrote:

> 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,
> Amanda

I'm still not quite getting what the system is. Are there bonds between
monomers? How many bonds are on each polymer? Have you been able to
simulate a regular polymer melt? What have you tried so far? My suggestion
is to start with a simpler system first and then work your way up to this
more complex system.

[ pairs ] is just for 1-4 non-bonded interactions. Do you want those in
your simulation? This all depends on what you have in [ defaults ] as well.
Do you have "gen-pairs" as yes? Are you excluding 1-4 non-bonded
interactions? Do you even have those in your system? From your description
above it looks like you have just two particles per molecule, so non-bonded
interactions between particles in the same molecule would be irrelevant.

[ nonbonded_params ] will override any previous combination rule. In this
section you must specify every interaction's parameters.

The simple answer to this question is - if you want different interactions
between different monomers, they need to be different atom types, and most
likely you'll want to specify each interaction in [ nonbonded_params ].

> ----------------------------
> > ​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
> polymer?
> --
> 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
> http://wbarnett.us
> ----------------------------
> Hi,
> 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.
> Cheers,
> Yu
> --
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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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