Molecular Dynamics (MD) is a theoretical simulation method for studying classical statistical
mechanics of welldefined systems through numerical solutions of Newton's equations of motion.
In our laboratory, we use it to perform interpretation of Raman and EXAFS spectra.
In the EXAFS spectra case, the use of MD allows us to overcome problems related to
accurate accounting for disorder effects, in particular, beyond the first coordination
shell  in the region, where the multiplescattering (MS) effects, depending on manyatom
distributions, contribute.
Other examples:
A. Anspoks, A. Kalinko, R. Kalendarev, A. Kuzmin,
Atomic structure relaxation in nanocrystalline NiO studied by EXAFS spectroscopy: Role of nickel vacancies,
Phys. Rev. B 86 (2012) 174114:111.
J. Timoshenko, A. Kuzmin, J. Purans,
Molecular dynamics simulations of EXAFS in germanium,
Centr. Eur. J. Phys. 9 (2011) 710715.
A. Kuzmin, V. Efimov, E. Efimova, V. Sikolenko, S. Pascarelli, I. O. Troyanchuk,
Interpretation of the Co Kedge EXAFS in LaCoO_{3} using molecular dynamics simulations,
Solid State Ionics 188 (2011) 2124.
A. Kalinko, R.A. Evarestov, A. Kuzmin, J. Purans,
Interpretation of EXAFS in ReO_{3} using molecular dynamics simulations,
J. Phys.: Conf. Ser. 190 (2009) 012080 (4pp).
USEFUL LINKS
Wikipedia: Molecular dynamics.
GULP  the General Utility Lattice Program.
LAMMPS  a Largescale Atomic/Molecular Massively Parallel Simulator.
HOOMDblue  a generalpurpose particle simulation toolkit.
DL_POLY  a general purpose serial and parallel molecular dynamics simulation package.
IMD  a software package for classical molecular dynamics simulations.
XMD  Molecular Dynamics for metals and ceramics.
OpenMD  an open source molecular dynamics engine.
PIMD  an opensource software for parallel molecular simulations.
XenoView  a Windows based software for molecular dynamics simulations..
CP2K  a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems.
CPMD  a parallelized plane wave / pseudopotential implementation of Density Functional Theory, designed for abinitio molecular dynamics.
OpenKIM  the knowledgebase of interatomic models.
Database of Published Interatomic Potential Parameters.
Interatomic Potentials Repository Project at NIST.
JARVIS Forcefields at NIST.
Atomicrex  a tool for the construction of interaction models.
atsim.potentials  a tool for potential model tabulation.
Potfit  a free implementation of the forcematching algorithm to generate effective potentials from abinitio reference data.
GARFfield  a multiplatform, multiobjective parallel hybrid genetic algorithm (GA) / conjugategradient (CG) based force field optimization framework.
PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space.
VESTA  a 3D visualization program for structural models and 3D grid data such as electron/nuclear densities.
VMD  a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3D graphics and builtin scripting.
Ovito  scientific visualization and analysis software for atomistic simulation data.
MOLEKEL  an opensource multiplatform molecular visualization program.
GDIS  a GTK based program for the display and manipulation of isolated molecules and periodic systems.
Travis  trajectory analyzer and visualizer.
Atomsk  a commandline program that aims at creating, manipulating, and converting atomic systems, for the purposes of ab initio calculations, classical potential simulations, or visualization.
POVRay  the Persistence of Vision Raytracer, a tool for producing highquality computer graphics.
Engineering Virtual Organization for Cyber Design.
Materials Square.
Accelrys.
LAMMPS tutorials.
