Hi Lammps users
I have been working to run some simulations on a system with a polyatomic cation (NH4+), starting by testing the parameter set (taken from force constants in the literature). Along the way I have run into some difficulties. It seems that if I want to use a Morse or harmonic potential for the N-H bonds, and an angular potential for the HNH angle then "special-bonds" turns off the coulombic interaction between these atoms. Because of this I cannot converge my coulomb cutoff, and the system diverges in energy with respect to cutoff size. I can use special-bonds to turn the coulomb interaction back on, but this then means I have to modify my bond and angle potentials. I should also mention that I am new to pair potential simulations.
I am wondering if anybody can comment about this and provide workarounds, advice.
Thanks
Chris Taylor
What is the model you are trying to simulate? I.e. what
is the combination of bond,angle and pairwise interactions
you want?
Steve
I wanted to let the NH4+ molecule interact with anions and polar molecules through 1/4+ charges on the H atoms and Buckingham potentials for intermolecular H-H as well as H-anion, yet at the same time I wanted to use the Morse or harmonic potential to control the NH bond strengths. Special bonds seemed to be preventing the H atoms within the NH4+ molecule from "seeing each other Coulombically" and I think this is what caused energy divergence (there is an anion in the cell such that the charges are overall neutral).
To try to get around this I set special_bonds so that all of the Coulomb interactions were unscreened, and created a new Morse potential for NH overlaid with Buckingham HH and NH potentials, by fitting to some first-principles data.
Chris
Steve Plimpton wrote:
Special bonds seemed to be preventing the H atoms within the NH4+ molecule from "seeing each other Coulombically" and I >think this is what caused energy divergence (there is an anion in the cell such that the charges are overall neutral).
Well, that is what special_bonds is supposed to do. It has settings
to turn on/off both LJ and
Coulombic interactions in the same molecule. It will not affect
interactions between
atoms on different molecules or with free ions. Are you saying it is doing
something unexpected?
To try to get around this I set special_bonds so that all of the Coulomb interactions were unscreened, and created a new >Morse potential for NH overlaid with Buckingham HH and NH potentials, by fitting to some first-principles data.
This sounds reasonable. You can use pair hybrid overlay to use multiple LAMMPS
pair potentials if that is helpful.
Steve