Velocity rescaling

NAMD allows the user to equilibrate a system to a specified temperature by periodically rescaling the velocities of all particles such that a specified temperature is achieved. This rescaling is achieved by first applying the integration scheme to obtain a set of velocities for timestep n. These velocities are then rescaled to the desired temperature by multiplying by the factor

$$\sqrt{\frac{T_0}{T_{\text{ave}}}}$$

where

• T₀ = the desired temperature specified using the configuration option rescaleTemp
• $T_{\text{ave}}$ = the average temperature since the last velocity rescaling

The positions for timestep n+1 are then obtained by using these new velocities.

Temperature rescaling may be used with either the Verlet integrator or Langevin dynamics. The number of timesteps between rescalings is specified using the configuration parameter rescaleFreq.