steer¶
Specifies parameters for steered MD to bring C-termini close to their connection points
Single-valued attributes:
cpu-override: Override namd3 processor type since GPUresident namd3 cannot handle restraints (yet) (default: True)
ensemble: Name of ensemble to run in; note that NPT can only be performed on a solvated system (default: NVT)
force_constant: force constant (kcal/mol/Angstrom^2) (default: 20)
target_distance: distance (Angstrom) between carbonyl carbon of loop C-terminus and amide nitrogen of connecting residue that steered MD drives to (default: 2)
nsteps: number of MD time steps for steeering (default: 1000)
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 (only used if ensemble is NPT) (default: 100)
temperature: Temperature used in steered MD run (default: 300)
pressure: Pressure used in steered MD run (only used if ensemble is NPT) (default: 1)
receiver_flexible_zone_radius: size of zone around receiver N-terminal N in which CA’s are not fixed during steered MD (default: 0.0)
Subattribute: