LAMMPS framework for dynamic bonding and an application modeling DNA

Published: 01-08-2012| Version 1 | DOI: 10.17632/g965bpw9cd.1
Carsten Svaneborg


This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected tri... Title of program: LAMMPS Framework for Directional Dynamic Bonding Catalogue Id: AEME_v1_0 Nature of problem Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Versions of this program held in the CPC repository in Mendeley Data AEME_v1_0; LAMMPS Framework for Directional Dynamic Bonding; 10.1016/j.cpc.2012.03.005