.. _dynamics:

========
Dynamics
========

Molecular dynamics based upon Newton's classical equations of motion.

[Dynamics] Options
==================

**time_step**: The duration of each MD step, in femtoseconds.

   default: ``1``

**time**: How long the MD simulation will be performed, in femtoseconds.

   default: ``1000.0``

**thermostat**

   default: ``none``

   options:

       ``none``: NVE dynamics with the verlet algorithm. Initial velocities set by temperature.

       ``andersen``: Andersen thermostat with the Verlet algorithm.

       ``langevin``: Langevin thermostat with the Verlet algorithm.

..       ``nose_hoover``: Nosé-Hoover thermostat with the Verlet algorithm.

**andersen_collision_period**: The collision period (in fs) for the
Andersen thermostat.

   default: ``100.0``
 
**andersen_alpha**: The collision strength in the Andersen thermostat.

   default: ``1.0``

..    **nose_mass**: The effective mass of the additional degree of freedom in the
     Nosé-Hoover thermostat, which determines the coupling frequency of the thermostat.

..   default: ``1.0``

**langevin_friction**: The damping coefficient for Langevin dynamics (1/fs).

   default: ``0.01``