Difference between revisions of "GROMACS"

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It 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]].
 
It 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]].
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Further information can be found in the wiki dedicated to GROMACS: [http://wiki.gromacs.org/ wiki.gromacs.org].
 
==References==
 
==References==
 
#[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)]
 
[[Category: Materials modeling and Computer simulation codes]]
 
[[Category: Materials modeling and Computer simulation codes]]

Revision as of 14:09, 3 August 2007

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.

It 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)