Molecular Dynamics



Molecular Dynamics (MD) is a theoretical simulation method for studying classical statistical mechanics of well-defined 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 multiple-scattering (MS) effects, depending on many-atom distributions, contribute.



Example of MD simulation of SrTiO3 at room temperature

(from A. Kuzmin and R.A. Evarestov, J. Phys.: Condens. Matter 21 (2009) 055401)




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) 174114:1-11.

  • J. Timoshenko, A. Kuzmin, J. Purans,
    Molecular dynamics simulations of EXAFS in germanium,
    Centr. Eur. J. Phys. 9 (2011) 710-715.

  • A. Kuzmin, V. Efimov, E. Efimova, V. Sikolenko, S. Pascarelli, I. O. Troyanchuk,
    Interpretation of the Co K-edge EXAFS in LaCoO3 using molecular dynamics simulations,
    Solid State Ionics 188 (2011) 21-24.

  • A. Kalinko, R.A. Evarestov, A. Kuzmin, J. Purans,
    Interpretation of EXAFS in ReO3 using molecular dynamics simulations,
    J. Phys.: Conf. Ser. 190 (2009) 012080 (4pp).





  • USEFUL LINKS

  • GULP - the General Utility Lattice Program.
  • MOLDY - a general-purpose Molecular Dynamics simulation program.
  • DL_POLY - a general purpose serial and parallel molecular dynamics simulation package.
  • LAMMPS - a Large-scale Atomic/Molecular Massively Parallel Simulator.
  • IMD - a software package for classical molecular dynamics simulations.
  • XMD - Molecular Dynamics for metals and ceramics.
  • OpenMD - an open source molecular dynamics engine.

  • 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 ab-initio molecular dynamics.

  • Database of Published Interatomic Potential Parameters.
  • OpenKIM - an online suite of open source tools for molecular simulation of materials.


  • 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 3-D graphics and built-in scripting.
  • MOLEKEL - an open-source multi-platform 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 command-line program that aims at creating, manipulating, and converting atomic systems, for the purposes of ab initio calculations, classical potential simulations, or visualization.

  • POV-Ray - the Persistence of Vision Raytracer, a tool for producing high-quality computer graphics.


  • Molecular Dynamics Simulation Packages.


  • Accelrys.







  • This page is maintained by Alexei Kuzmin (a.kuzmin@cfi.lu.lv).