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338 Database entries



NAMD


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OS: Linux, Windows, Mac, ...

License: Freeware, Registration



Methods: MD


NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.


Features:

Molecule Building

* VMD used to prepare molecular structure for simulation.
* Also reads X-PLOR, CHARMM, AMBER, and GROMACS input files.
* Psfgen tool generates structure and coordinate files for CHARMM force field.
* Efficient conjugate gradient minimization.
* Fixed atoms and harmonic restraints.
* Thermal equilibration via periodic rescaling, reinitialization, or Langevin dynamics.

Basic Simulation

* Constant temperature via rescaling, coupling, or Langevin dynamics.
* Constant pressure via Berendsen or Langevin Nose-Hoover methods.
* Particle mesh Ewald full electrostatics for periodic systems.
* Symplectic multiple timestep integration.
* Rigid waters and bonds to hydrogen atoms.

Advanced Simulation

* Chemical and conformational free energy calculations.
* Locally enhanced sampling via multiple images.
* Tcl based scripting and steering forces.
* Analysis implemented as Tcl scripts in VMD.
* Interactive visual steering interface to VMD.

Scalable Performance

* Based on the Charm++/Converse parallel runtime system.
* Spatial data decomposition for limited communication pattern.
* Message driven execution for latency tolerance on commodity networks.
* Measurement-based load balancing for scaling to hundreds of processors.
* Largest simulation to date is over 300,000 atoms on 1000 processors.

http://www.ks.uiuc.edu/Research/namd/



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