GROMACS
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
References
- H. J. C. Berendsen, D. van der Spoel and R. van Drunen "GROMACS: A message-passing parallel molecular dynamics implementation", Computer Physics Communications 91 pp. 43-56 (1995)
- David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen "GROMACS: Fast, flexible, and free", Journal of Computational Chemistry 26 pp. 1701-1718 (2005)
- Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", Journal of Chemical Theory and Computation 4 pp. 435–447 (2008)