GROMACS at NNIN
GROMACS at NNIN
Overview:
Gromacs is an open source parallel molecular dynamics code that uses classical Newtonian mechanics to simulate the interactions of hundreds to millions of particles.
Applications:
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.
Developers:
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.
Getting Started:
- 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).
Questions, Comments...
Please contact:
Derek Stewart, Ph.D.
stewart (at) cnf.cornell.edu
Cornell Nanoscale Facility