In the limit of high friction, stochastic dynamics reduces to Brownian
dynamics, also called position Langevin dynamics. This applies to
over-damped systems, i.e. systems in which the inertia effects are
negligible. The equation is
where is Gaussian distributed
noise with , . The friction
coefficients can be chosen the same for all particles
or as , where the friction constants
can be different for different groups of atoms. Because
the system is assumed to be over-damped, large timesteps can be used.
LINCS should be used for the constraints since SHAKE will not converge
for large atomic displacements. BD can be activated by using
integrator=bd and the simulations are run using the
mdrun program.
In BD there are no velocities, so there is also no kinetic energy. Still
gmx mdrun will report a kinetic energy and temperature based on
atom displacements per step . This can be used to judge
the quality of the integration. A too high temperature is an indication
that the time step chosen is too large. The formula for the kinetic
energy term reported is: