On 09/21/09, xiao shijun <[email protected]> wrote: > > Mark wrote: > > xiao shijun wrote: > > >> Hi everyone, > >> Recently, I met a problem on the force-field. I am doing something > >> on the calcium carbonate, and want to simulation it with gromacs. > >> The shell model for oxygen has been emploied in my system. When I > >> considered the non-boned potential associated with interactions between > >> atoms > >> in the same CO3 group, I only need to take O-O buckingham interaction > >> into account, but any electric interaction. How could I realize that in > >> my .top file. > >> First, I tried to use [pairs] to eliminate electric interaction, but > >> I can't add the buckingham interaction of O-O because there is no > >> buckingham > >> options for LJC14. I want to know if anyone of you have such the > >> experience. Thanks!! > > >Usually you would not define a nonbonded interaction for atoms that > are > >so close together, since their interaction should be able to be > modelled > >adequately with the C-O bond and O-C-O angle (and perhaps with CHARMM, > >an interaction harmonic the O-O distance as a Urey-Bradley term). > > Thanks for Mark's suggestion. But I want to reproduce the simulation from > the other paper, > The paper describe the force-field that O-O nonbonded interaction in the > same carbonate should be considered. > In addition to that, I can't use buckingham potential in [pairs], even > choose funct = 2. I am wondering > if I want to describe 1-4 interaction by Buckingham, what could I do? This is one application for setting nrexcl for moleculetypes. You don't want exclusions for particles 2 bonds apart, so set this to one. See chapter 5.
If that doesn't work, then if the "bonded" interactions are merely harmonic distance potentials, then GROMACS permits a form of them that doesn't create a bond (bond type 6, IIRC, check chapter 5; or constraint type 2). Thus, the automated exclusion mechanism won't be involved, and you can have Buckingham O-O so long as you have Buckingham for all other LJ interactions. You will need manual exclusions for C-O pairs, I guess. Thus [ atomtypes ] C #nonbonded parameters go here O #nonbonded parameters go here [moleculetype] carbonate [atoms] C O1 O2 O3 [bonds] C-O1 # type 6 C-O2 # type 6 C-O3 # type 6 [exclusions] 1 2 1 3 1 4 Whether this works may depend on whatever else is in your system, though. Mark
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