Difference between revisions of "GROMACS"

From SklogWiki
Jump to: navigation, search
m (Added GROMACS on Tesla GPUs section)
m (Added a note on the Constraint algorithms)
Line 7: Line 7:
 
==GROMACS on Tesla GPUs==
 
==GROMACS on Tesla GPUs==
 
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>
 
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>
 +
==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>.
 
==References==
 
==References==
 
<references/>
 
<references/>

Revision as of 13:28, 27 July 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]

Constraint algorithms

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

References

External links