Brownian Dynamics
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
(117)
where is the friction coefficient
and
is a noise
process with
.
In GROMACS the equations are integrated with a simple, explicit scheme
(118)
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 is an option of the mdrun program.