NAMD Example
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.
This is a simple example of a molecular dynamics simulation on Rescale.
| Simulation Code | NAMD v2.11 tcp |
| Analysis Type | Molecular dynamics |
| Description | Molecular dynamics (MD) simulations to compute atomic trajectories by solving empirical force field equations that approximate the actual atomic force in biopolymer systems. |
| Suggested Hardware | Titanium / 1 cores |
| Command |
namd2 bpti_namd_script |
| Estimated Run Time | 2 minutes |