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
.. math:: {{\mbox{d}}\mathbf{r}_i \over {\mbox{d}}t} = \frac{1}{\gamma_i} \mathbf{F}_i(\mathbf{r}) + {\stackrel{\circ}{\mathbf{r}}}_i
:label: eqnbrowniandyn
where :math:`\gamma_i` is the friction coefficient
:math:`[\mbox{amu/ps}]` and
:math:`{\stackrel{\circ}{\mathbf{r}}}_i\!\!(t)` is a noise
process with
:math:`\langle {\stackrel{\circ}{r}}_i\!\!(t) {\stackrel{\circ}{r}}_j\!\!(t+s) \rangle = 2 \delta(s) \delta_{ij} k_B T / \gamma_i`.
In |Gromacs| the equations are integrated with a simple, explicit scheme
.. math:: \mathbf{r}_i(t+\Delta t) = \mathbf{r}_i(t) +
{\Delta t \over \gamma_i} \mathbf{F}_i(\mathbf{r}(t))
+ \sqrt{2 k_B T {\Delta t \over \gamma_i}}\, {\mathbf{r}^G}_i,
:label: eqnbrowniandynint
where :math:`{\mathbf{r}^G}_i` is Gaussian distributed
noise with :math:`\mu = 0`, :math:`\sigma = 1`. The friction
coefficients :math:`\gamma_i` can be chosen the same for all particles
or as :math:`\gamma_i = m_i\,\gamma_i`, where the friction constants
:math:`\gamma_i` 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 :ref:`mdrun ` program.