Difference between revisions of "GROMACS"

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#[http://dx.doi.org/10.1016/0010-4655(95)00042-E  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)]
 
#[http://dx.doi.org/10.1016/0010-4655(95)00042-E  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)]
 
#[http://dx.doi.org/10.1002/jcc.20291 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)]
 
#[http://dx.doi.org/10.1002/jcc.20291 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)]
 +
#[http://dx.doi.org/10.1021/ct700301q 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)]
 
[[Category: Materials modelling and computer simulation codes]]
 
[[Category: Materials modelling and computer simulation codes]]

Revision as of 11:05, 5 May 2009

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 nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Further information can be found in the wiki dedicated to GROMACS: wiki.gromacs.org.

References

  1. 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)
  2. 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)
  3. 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)