Loading src/USER-REACT/README 0 → 100644 +23 −0 Original line number Diff line number Diff line This package implements the DisARMMD protocol (disarmmd.org) as "fix bond/react." This fix allows for complex topology changes during a running MD simulation, when using classical force fields. Topology changes are defined in pre- and post-reaction molecule templates and can include creation and deletion of bonds, angles, dihedrals, impropers, atom types, bond types, angle types, dihedral types, improper types, and/or atomic charges. The DisARMMD protocol is a method for modeling chemical reactions in classical molecular dynamics simulations. It was developed to build physically-realistic initial configurations for amorphous or crosslinked materials. Any number of competing or reversible reaction pathways can be specified, and reacting sites can be stabilized. Other advanced options currently available include reaction constraints (e.g. angle and Arrhenius constraints), deletion of reaction byproducts or other small molecules, and chiral-sensitive reactions. The DisARMMD methodology is detailed in: Gissinger et al., Polymer 128, 211-217 (2017) https://doi.org/10.1016/j.polymer.2017.09.038 This package was created by Jacob Gissinger (info@disarmmd.org), while at the NASA Langley Research Center. Loading
src/USER-REACT/README 0 → 100644 +23 −0 Original line number Diff line number Diff line This package implements the DisARMMD protocol (disarmmd.org) as "fix bond/react." This fix allows for complex topology changes during a running MD simulation, when using classical force fields. Topology changes are defined in pre- and post-reaction molecule templates and can include creation and deletion of bonds, angles, dihedrals, impropers, atom types, bond types, angle types, dihedral types, improper types, and/or atomic charges. The DisARMMD protocol is a method for modeling chemical reactions in classical molecular dynamics simulations. It was developed to build physically-realistic initial configurations for amorphous or crosslinked materials. Any number of competing or reversible reaction pathways can be specified, and reacting sites can be stabilized. Other advanced options currently available include reaction constraints (e.g. angle and Arrhenius constraints), deletion of reaction byproducts or other small molecules, and chiral-sensitive reactions. The DisARMMD methodology is detailed in: Gissinger et al., Polymer 128, 211-217 (2017) https://doi.org/10.1016/j.polymer.2017.09.038 This package was created by Jacob Gissinger (info@disarmmd.org), while at the NASA Langley Research Center.
