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

Du, Yu duyu at sioc.ac.cn
Fri Sep 29 02:26:16 CEST 2017


Before the simulation of monomers polymerizing, you can try some tentative experiments, such dimerization and trimerization. If the simulation of trimerization succeeds, you really don't need the further experiment because the trimerization simulation is strong to support the further polymerization process because trimerization include the comformation change after dimerization and other important information.

Carefully design the size of the box to avoid the lenth of the polymer exceeding some dimension of the box whose size is fixed according to the preset seperated monomers, espesially in the case of trimer or larger numbers of monomers.

For PLUMED, 1) In the case of dimer, trimer or larger, you can use BIASVALUE to apply user-defined bias function between the A and B of different monomers. The bias function can choose to be that if the monomers are distant from each other the bias force is large, if near then the force is small to exclude the artifial bias effect.
2) In the case of dimer, you can also try the funnel metadynamics, which you can search for more information.

if you are simulating biological system, yours resembles the actin filament, you can search related simulation paper to check if there are published cases to study.


> -----Original Messages-----
> From: "Amanda Parker" <asparker at ucdavis.edu>
> Sent Time: 2017-09-29 01:10:20 (Friday)
> To: gmx-users at gromacs.org
> Cc: 
> Subject: Re: [gmx-users] manually adding non-bonded interactions based on atom number to topology file
> 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
> ----------------------------
> > ​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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Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

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