Simulations

Introduction

Assorted topics relevant to programming particle-based simulation codes and to using these codes for the modeling of a wide range of systems, notably complex fluids.

Molecular dynamics simulations

Special Usage Notes

By default LAMMPS normalizes the temperature by an amount dof – d, where dof is the system's total number of degrees of freedom and d is the dimensionality of the simulation. Subtracting d accounts for the center-of-mass motion of the system. This is correct except when there is a proper frame of reference for the system, e.g., in a Langevin dynamics simulation in which the implicit background solvent has zero average velocity. In this case it is necessary to use the command compute_modify to ensure dof is used instead of dof – d. For instance one can use

compute myTemp all temp
compute_modify myTemp extra 0
thermo_modify temp myTemp