Difference between revisions of "GROMACS"

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'''GROMACS''' is a versatile package to perform [[molecular dynamics]], i.e. simulate the  
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'''GROMACS''' <ref>[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)]</ref>
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<ref>[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)]</ref>
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<ref>[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)]</ref>
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is a versatile package to perform [[molecular dynamics]], i.e. simulate the  
 
[[Newtons laws |Newtonian equations of motion]] for systems with hundreds to millions of particles.
 
[[Newtons laws |Newtonian equations of motion]] for systems with hundreds to millions of particles.
 
GROMACS is primarily designed for [[Biological systems |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]].
 
GROMACS is primarily designed for [[Biological systems |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]].
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==GROMACS on Tesla GPUs==
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The CUDA port of GROMACS enabling GPU acceleration is now available in beta and supports [[Ewald sum#Particle mesh|Particle-Mesh-Ewald]], arbitrary forms of non-bonded interactions, and implicit solvent Generalized Born methods <ref> source: [http://www.nvidia.com/object/gromacs_on_tesla.html NVIDIA]</ref>
 
==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)]
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<references/>
*[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)]
 
 
==External links==
 
==External links==
 
*[http://www.gromacs.org/ GROMACS home page]
 
*[http://www.gromacs.org/ GROMACS home page]
 
[[Category: Materials modelling and computer simulation codes]]
 
[[Category: Materials modelling and computer simulation codes]]

Revision as of 15:17, 10 May 2010

GROMACS [1] [2] [3] 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.

GROMACS on Tesla GPUs

The CUDA port of GROMACS enabling GPU acceleration is now available in beta and supports Particle-Mesh-Ewald, arbitrary forms of non-bonded interactions, and implicit solvent Generalized Born methods [4]

References

External links