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Difference between revisions of "Molecular Modeling"
From Cluster Documentation Project
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* [http://deshawresearch.com/resources.html Desmond] is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer. | * [http://deshawresearch.com/resources.html Desmond] is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer. | ||
* [http://charm.cs.uiuc.edu/OpenAtom/ OpenAtom] is a highly scalable and portable parallel application for molecular dynamics simulations at the quantum level. It implements the Car-Parrinello ab-initio Molecular Dynamics (CPAIMD) method. OpenAtom is written using the [http://charm.cs.uiuc.edu/ Charm++] parallel programming framework. It runs on a variety of architectures like PowerPC, Opteron and Intel-based systems. | * [http://charm.cs.uiuc.edu/OpenAtom/ OpenAtom] is a highly scalable and portable parallel application for molecular dynamics simulations at the quantum level. It implements the Car-Parrinello ab-initio Molecular Dynamics (CPAIMD) method. OpenAtom is written using the [http://charm.cs.uiuc.edu/ Charm++] parallel programming framework. It runs on a variety of architectures like PowerPC, Opteron and Intel-based systems. | ||
| + | *[http://www.scripps.edu/mb/olson/doc/autodock/ AutoDock] is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid re-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders. | ||
Revision as of 20:31, 21 July 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. 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.
- NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats.
- Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.
- OpenAtom is a highly scalable and portable parallel application for molecular dynamics simulations at the quantum level. It implements the Car-Parrinello ab-initio Molecular Dynamics (CPAIMD) method. OpenAtom is written using the Charm++ parallel programming framework. It runs on a variety of architectures like PowerPC, Opteron and Intel-based systems.
- AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid re-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.
