On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm.

Widely used programs for molecular dynamics simulation of (bio)molecular systems are the Verlet and leapfrog algorithms. In these algorithms, the particle velocities are less accurately propagated than the positions. Important quantities for the simulation such as the temperature and the pressure involve the squared velocities at full time steps. Here, we derive an expression for the squared particle velocity at full time step in the leapfrog scheme, which is more accurate than the standardly used one. In particular, this allows us to show that the full time step kinetic energy of a particle is more accurately computed as the average of the kinetic energies at previous and following half steps than as the square of the average velocity as implemented in various molecular dynamics codes. Use of the square of the average velocity introduces a systematic bias in the calculation of the instantaneous temperature and pressure of a molecular dynamics system. We show the consequences when the system is coupled to a thermostat and a barostat.