GROMACS at NNIN
GROMACS at NNIN
Gromacs is an open source parallel molecular dynamics code that uses classical Newtonian mechanics to simulate the interactions of hundreds to millions of particles.
Gromacs was primarily designed to study biochemical molecules (proteins, lipids, and nucleic acids) with challenging bonded interactions. However, recently several groups have used to study non-biological systems such as polymers.
Development on the GROMACS package was first led by Herman Berendsens' group in the Department of Biophysical Chemistry of Groningen University, The Netherlands.
The current developers of the code are:
- Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, Sweden)
- David van der Spoel (Biomedical Centre, Uppsala, Sweden)
- Berk Hess (Max Planck Institute for Polymer Research, Mainz, Germany)
- Gerrit Groenhof (Max Planck Institute for Polymer Research, Mainz, Germany)
- Carsten Kutzner (Max Planck Institute for Polymer Research, Mainz, Germany)
A list of former developers who have contributed to GROMACS can be also be found here.
- The Main Gromacs Webpage
- Gromacs 4.0 Online Reference
- Gromacs Tutorials
- Simulating Carbon Nanotubes with Gromacs
- Justin Lemkul's (Virginia Tech) Gromacs Tutorials: Lysosyme in Water and Membrane Protein
Relevant Research Articles and Webpages:
- "GROMACS: A message-passing parallel molecular dynamics implementation", H. J. C. Berendsen, D. van der Spoel, and R. van Drunen, Computer Physics Communications 91, 43 (1995).
- "GROMACS 3.0: a package for molecular simulation and trajectory analysis", E. Lindahl, B. Hess, and D. van der Spoel, Journal of Molecular Modeling 7, 306 (2001).
- "GROMACS: Fast, flexible, and free", D. van der Spoel, E. Lindahl, B. Hess, G. Groenhor, A. E. Mark, H. J. C. Berendsen, Journal of Computational Chemistry 26 1701 (2005).
- "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation", B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, Journal of Chemical Theory and Computation, 4, 435 (2008).
Derek Stewart, Ph.D.
stewart (at) cnf.cornell.edu
Cornell Nanoscale Facility