DL_MESO_DPD Jargon

Below shows definitions that are related to DL_MESO_DPD, or indeed, generally to dissipative particle dynamics (DPD) simulations.

• CONFIG - An (optional) DL_MESO_DPD file that stores the location state of particles in a system model, including positions, forces and velocities.

• FIELD - A DL_MESO_DPD file that describes the force field (interaction) model of a system, including particle content, molecular topology and applied external fields.

• CONTROL - A DL_MESO_DPD file that contains a set of directives to drive the DPD simulation process.

• particle or bead - Any entity occupying a unique entry in the CONFIG and FIELD files. It is a countable object and has a global ID index. In the case of DPD, it can be either a coarse-grained representation of selected atoms or a mesoscopic representation of a continuum fluid (a ‘carrier of momentum’).

• intra-molecular interactions - Interaction components that involve connectivity of particles within a molecule. For example, chemical (stretching) bonds, angles involving three particles, dihedrals and impropers involving four particles.

• inter-molecular interactions - Interaction components that do not directly involve covalent bonds, acting between individual beads or molecules. For example: conservative (van-der-Waals) interactions, many-body DPD potentials, electrostatic interactions.