Chemistry Reference
In-Depth Information
The most time consuming part of MD simulations are the non-bonded
interactions. The potential functions calculations include Coulomb potential
function and Lennard-Jones potential functions. Non-bonded interactions use a
cutoff radius, which commonly does not exceed half the shortest box vector for
grid search. This avoids interactions between particles and their images at the
same time. Half the side length of the cell used for cubic simulations boxes.
Ewald sums and reaction-field approaches can handle long-range interactions
(strong decay with distance). The Ewald interaction potential is the sum of a
short-range term in real space and a Fourier space long-range term, which
assumes an infinitely periodic system and specified by a dielectric constant
medium
In the simulation box, the field on a dipole in the reaction-field approximation is
divided into a cavity and a surrounding medium of electrostatic interactions
summed explicitly in the cavity. The surrounding medium should be given a
dielectric constant and act as a smooth continuum. Outside the cutoff sphere of
atom/charge group, the medium is modeled as a dielectric continuum (specified
relative permittivity) which modifies the Coulomb electrostatic interactions. The
method yields polarization of the surrounding continuum and the reaction field on
the molecule at the center.
Using a thermostat algorithm the NVT MD simulation is adequate to investigate
the behavior of the system at a specific temperature (experimental conditions).
One of the first MD thermostats is attributed to Anderson [573]. The desired T is
replaced using a stochastic collision method in which Maxwell-Boltzmann
distribution yields, randomly, the velocity of the particle. The method gives a
distribution of energies of 'mini-microcanoncal' simulations.
For the thermostats algorithms of Berendsen (velocity scaling) [574], the system
is coupled to a fixed temperature external heat bath whereas the velocities scaled
at each step. Extended systems introduced by Nose and Hoover [575]. Berendsen
and Parrinello-Rahaman [576] introduced common used barostats for pressure
control in MD simulations.
