Difference between revisions of "GROMACS"

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==Constraint algorithms==
 
==Constraint algorithms==
 
GROMACS can use either the [[SHAKE]] or the [[LINCS]] algorithms <ref>[http://www.gromacs.org/@api/deki/files/82/=gromacs4_manual.pdf GROMACS 4 Manual] &sect; 3.6 </ref>.
 
GROMACS can use either the [[SHAKE]] or the [[LINCS]] algorithms <ref>[http://www.gromacs.org/@api/deki/files/82/=gromacs4_manual.pdf GROMACS 4 Manual] &sect; 3.6 </ref>.
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==Force fields==
 +
GRMACS comes with the following [[force fields]] <ref>Source: /usr/share/gromacs/top for gromacs-4.5.5 </ref><ref>GROMACS 4.5.6 manual &sect; 4.10 </ref>
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* [[AMBER forcefield | AMBER]]
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** amber03
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** amber94
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** amber96
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** amber99
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** amber99sb
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** amber99sb-ildn
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** amberGS
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*[[CHARMM]]
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** charmm27
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*[[ENCAD (force field) | ENCAD]]
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** encads
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** encadv
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* gmx2
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* gmx
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*[[GROMOS]]
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** gromos43a1
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** gromos43a2
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** gromos45a3
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** gromos53a5
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** gromos53a6
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*[[MARTINI]]
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*[[OPLS force field | OPLS-all atom]]
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==References==
 
==References==
 
<references/>
 
<references/>

Revision as of 18:13, 5 November 2013

GROMACS [1] [2] [3] (GROningen MAchine for Chemical Simulations) 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]

Constraint algorithms

GROMACS can use either the SHAKE or the LINCS algorithms [5].

Force fields

GRMACS comes with the following force fields [6][7]

References

External links