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 At2017-09-28 08:07:54,Amanda Parker<aspar...@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. > > Thanks, > Amanda > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
