NAMD (NAnoscale Molecular Dynamics program) is a parallel molecular dynamics simulation package designed for high-performance simulation of large biomolecular systems. It has been implemented in C++ and based on Charm++ parallel programming model. NAMD scales to thousands of processors on high-end parallel platforms and can also be run on individual desktops and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats and includes a rich set of MD features (multiple time stepping, constraints, and dissipative dynamics). NAMD can be connected to the molecular graphics software VMD in order to provide an interactive simulation tool for modifying and viewing the running MD simulations.

 

Application/Keywords: Molecular Dynamics Simulations, Steered Molecular Dynamics, GPU acceleration, High-performance simulation, Enhanced Sampling