Simulations

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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 , where is the system's total number of degrees of freedom and is the system's dimensionality. Subtracting 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 is used instead of . 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.

Monte Carlo simulations