Hi, everyone,
I have a question on special bonds command. Does this command work with other pairwise potentials?
I read the information on special bonds command in the LAMMPS manual. According to the information, it seems that this command can be applied for lj, coul,amber,charmm,fene potentials. So how about other pairwise potentials, such as buckingham, born potentials? The reason I ask this question is that I’m building a molecule system. The force field describing the interactions in this system includes intramoleuclar and intermolecular interactions. Intramolecular interaction includes bond, angle, dihedral potentials. Intermolecular interaction is defined by buckingham potential plus coulombic potential. I hope the buckingham and coulombic potentials only describe the interaction of a pair of atoms in different molecules. If special bonds command works with buck/coul potentials, I don’t need do something special for excluding the intramolecular pairwise interaction since the default values for this command do the exclusion. Is my understanding right? If not, how can I do to exclude intramolecular pairwise interaction?
Your any suggestions are highly appreciated.
Hi, everyone,
I have a question on special bonds command. Does this command work with other pairwise potentials?
I read the information on special bonds command in the LAMMPS manual. According to the information, it seems that this command can be applied for lj, coul,amber,charmm,fene potentials. So how about other pairwise potentials, such as buckingham, born potentials? The reason I ask this question is that I’m building a molecule system. The force field describing the interactions in this system includes intramoleuclar and intermolecular interactions. Intramolecular interaction includes bond, angle, dihedral potentials. Intermolecular interaction is defined by buckingham potential plus coulombic potential. I hope the buckingham and coulombic potentials only describe the interaction of a pair of atoms in different molecules. If special bonds command works with buck/coul potentials, I don’t need do something special for excluding the intramolecular pairwise interaction since the default values for this command do the exclusion. Is my understanding right? If not, how can I do to exclude intramolecular pairwise interaction?
Helen:
The special_bonds command works with any pairwise interaction. The keywords “lj” and “coul” allow you to specify different values for the pairwise (default is usually an LJ potential) and the coulombic interactions. The other keywords—“amber,” “charmm,” and “fene”—allow you to specify quickly commonly used settings for these coefficients. However, you are free to specify another set of values that are consistent with the force field you select.
I still don’t get it how to set the weighting factors for arbitrary pairwise potential.
For instance, if I want to specify the weighting factors between Stillinger-Weber (sw) pairwise potential and bonding potentials as 0.6, 0.5, 0.4 (for 1-2, 1-3, 1-4 atom pairs respectively) , should I write the script as following?
Hi everyone,
I still don't get it how to set the weighting factors for arbitrary pairwise
potential.
For instance, if I want to specify the weighting factors between
Stillinger-Weber (sw) pairwise potential and bonding potentials as 0.6, 0.5,
0.4 (for 1-2, 1-3, 1-4 atom pairs respectively) , should I write the script
stillinger weber is not meant to be used with bonded potentials.
as following?
"special_bonds sw 0.0 0.0 0.5 "
no. have you seen this somewhere in the documentation?
special_bonds scaling can be applied to charges (coul) or
other non-bonded terms (lj) or both at the same time (lj/coul).
however, for those to be effective, the non-bonded potential
implementation must recognize those _and_ decode the
special_bond scaling factor from the neighborlist. none of
the many-body potentials does that, since they compute
their own bonded interactions on the fly.
if you want to have a many-body interaction with some fixed
bonds and scaled down non-bonded terms, then you'll have
to write a new pair style for that. it is a _very_ awkward model.
SW is not a pairwise potential (though LAMMPS calls it a pair style).
It makes no sense to use special_bonds with it, as there are no
permanent bonds in a SW potential. Same with Tersoff or any
other bond-order potential in LAMMPS. The SW potential
ignores any special_bond settings. Special bonds is use
to set weighting factors on pairs of atoms that are "bonded"
to each other permanently by a bond_style command (e.g.
harmonic, fene, etc).