NAMD
From HP-SEE Wiki
Contents |
- Web site: http://www.ks.uiuc.edu/Research/namd
- Described version: xx.xx
- Licensing: Free for non-commercial use, http://www.ks.uiuc.edu/Research/namd/license.html
- User documentation: link
- Download: link
- Source code: link
Authors/Maintainers
- Also origin, if the software comes from a specific project.
Summary
NAMD is a parallel classical molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit Ethernet. NAMD uses a specifically designed molecular graphics program VMD for simulation setup and analysis of MD trajectories that it generates, but is also file-compatible with AMBER, CHARMM, and X-PLOR. It is available as precompiled binaries for many platforms, including BlueGene/P and Origin2000. Using the source code, it could be built on any platform supporting MPI or Ethernet. Supports simulation varying from basic ones like 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 time step integration. It also enables performing of alchemical free energy calculations by gradual mutation of a subset of atoms of the studied systems from one state to another, using either the free energy perturbation or thermodynamics integration approach. Conformational free energy calculations are also possible within the collective variables module of the code. NAMD is implemented using the Converse runtime system, and the major components of NAMD are written in charm++. Converse provides machine-independent interface to all popular parallel computers as well as workstation clusters. Converse also implements a data-driven execution model, allowing parallel languages such as charm++ to support the dynamic behaviour of NAMD's chunk-based decomposition scheme. The dynamic components of NAMD are implemented in the charm++ parallel language. It is composed of collections of C++ objects, which communicate by remotely invoking methods on other objects. This supports the multi-partition decompositions in NAMD. Also data-driven execution adaptively overlaps communication and computation. Finally, NAMD benefits from charm++'s load balancing framework to achieve unsurpassed parallel performance. The largest simulation to date performed with NAMD is over 300,000 atoms on 1000 processors.
Features
- Listed features
Architectural/Functional Overview
- high level design info, how it works, performance - may be a link, or several links
Usage Overview
- If possible with small example - may be a link
Dependacies
- list of all relevant dependencies on other libraries
HP-SEE Applications
- CompChem
- ISyMAB
- MDSCS
- HC-HC-MD-QM-CS
Resource Centers
- BG, BG
- HPCG, BG
- IFIN_Bio, RO
- NCIT-Cluster, RO
Usage by Other Projects and Communities
- If any
