md¶
Parameters controlling a NAMD run
Single-valued attributes:
single-core: whether or not to run namd on a single core; if false, namd3 will be used if available and appropriate for the system size (default: False)
cpu-override: revert to cpu version of namd3 (default: False)
vacuum: if true, namd will run on a single node even if multiple nodes are allocated (default: False)
ensemble: Name of ensemble to run in; note that NPT can only be performed on a solvated system (default: NVT)
minimize: Number of minimization steps; ignored if ensemble is not ‘minimize’ (used with the ‘minimize’ command) (default: 1000)
nsteps: Number of MD time steps; ingored if ensemble is ‘minimize’ (used with the ‘run’ command) (default: 2000)
dcdfreq: number of time steps between configuration output to DCD file (default: 100)
xstfreq: number of time steps between cell size output to DCD file (default: 100)
temperature: Temperature (K) for NVT or NPT (default: 300)
pressure: Pressure (bar) for NPT; note that NPT can only be performed on a solvated system (default: 1)
other_parameters: key:value pairs for other namd2 configuration file statements
colvar_specs: colvar specifications; dict with keys ‘groups’, ‘distances’, and ‘harmonics’
Container-like attribute:
Subattributes: