namd¶
Parameters for a NAMD configuration script to be included in the package tarball
Single-valued attributes:
ensemble: Name of ensemble to run in; note that NPT can only be performed on a solvated system (default: NVT)
firsttimestep: First timestep number for the run (used in the ‘run’ command) (default: 0)
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)
outputenergies: number of time steps between energy output to log file (default: 1000)
dcdfreq: number of time steps between configuration output to DCD file (default: 1000)
xstfreq: number of time steps between cell size output to DCD file (default: 1000)
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
Container-like attribute:
Subattribute: