The Berendsen thermostat is an algorithm to re-scale the velocities of particles in
molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of th ...
simulations to control the simulation temperature.
Basic description
In this scheme, the system is weakly coupled to a
heat bath
In thermodynamics, heat is defined as the form of energy crossing the boundary of a thermodynamic system by virtue of a temperature difference across the boundary. A thermodynamic system does not ''contain'' heat. Nevertheless, the term is al ...
with some temperature. The thermostat suppresses fluctuations of the
kinetic energy
In physics, the kinetic energy of an object is the energy that it possesses due to its motion.
It is defined as the work needed to accelerate a body of a given mass from rest to its stated velocity. Having gained this energy during its acce ...
of the system and therefore cannot produce trajectories consistent with the
canonical ensemble
In statistical mechanics, a canonical ensemble is the statistical ensemble that represents the possible states of a mechanical system in thermal equilibrium with a heat bath at a fixed temperature. The system can exchange energy with the hea ...
. The temperature of the system is corrected such that the deviation exponentially decays with some time constant
.
:
Though the thermostat does not generate a correct
canonical ensemble
In statistical mechanics, a canonical ensemble is the statistical ensemble that represents the possible states of a mechanical system in thermal equilibrium with a heat bath at a fixed temperature. The system can exchange energy with the hea ...
(especially for small systems), for large systems on the order of hundreds or thousands of atoms/molecules, the approximation yields roughly correct results for most calculated properties. The scheme is widely used due to the efficiency with which it relaxes a system to some target (bath) temperature. In many instances, systems are initially equilibrated using the Berendsen scheme, while properties are calculated using the widely known
Nosé–Hoover thermostat, which correctly generates trajectories consistent with a canonical ensemble. However, the Berendsen thermostat can result in the
flying ice cube effect, an artifact which can be eliminated by using the more rigorous Bussi–Donadio–Parrinello thermostat; for this reason, it has been recommended that usage of the Berendsen thermostat be discontinued in almost all cases except for replication of prior studies.
See also
*
Molecular mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemi ...
*
Software for molecular mechanics modeling
References
Molecular dynamics
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