CSVR thermostat

One popular strategy to control temperature in NVT MD is to rescale atomic velocities ($\bold{v}_{i}$) at a certain predefined frequency by some factor in such a way that the total kinetic energy of the system

$E_{kin} = \frac{1}{2} \sum\limits_{i=1}^{N} m_i |\bold{v}_{i}|^2,$

is equal to the average kinetic energy corresponding to given temperature:

$\bar{E}_{kin} = \frac{1}{2}N_f k_B T$

where $N_f = 3N -3$ for 3D periodc and $N_f = 3N -3$ for non-linear molecular systems and math>N </math> is the number of atoms. Such a method, however, suffers from several issues. First of all, the ensemble generated is not strictly canonical. Also, the trajectories generated via this naive rescaling method often suffer from flying ice-cube problem where kinetic energy vibrational degrees of freedom is transferred into translations and/or rotations, violating thus equipartition principle.

An elaborated approach based on the velocity rescaling has been proposed by Bussi et al.