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

By and large the CSML uses LAMMPS for MD, though depending on the application NAMD, GROMACS, or any of a host of other packages may be useful. Most issues can be resolved by consulting the LAMMPS manual, though some common problems are addressed below.

LAMMPS Special Usage Notes

• By default LAMMPS normalizes the temperature by an amount $n_{\text{dof}}-d$, where $n_{\text{dof}}$ is the system's total number of degrees of freedom and $d$ is the system's dimensionality. Subtracting $d$ accounts for the center-of-mass motion of the system. This leads to an incorrect reported value if the system has a proper frame of reference, e.g., when using a Langevin thermostat in which all particles interact with a stationary background solvent. In this case it is necessary to ensure $n_{\text{dof}}$ is used instead of $n_{\text{dof}}-d$. To do this, use compute_modify as follows

  compute myTemp all temp
  compute_modify myTemp extra 0
  thermo_modify temp myTemp
  

  As a note, the above only affects the reported temperature. The dynamics are computed correctly regardless.