NAMD Advanced Controls

This page collects controls that are not needed in a standard NAMD input. Start with the four named scheme values in the main [md] manual. Add an option from this page only when the chosen physical treatment, diagnostic comparison, or restart procedure requires it.

Initial Electronic-State Index

Use a state label such as namd(S1,...) in normal concise input. The lower-level active keyword selects the initial 1-based response-state index and defaults to 1. A state label is clearer and takes precedence when both forms are present.

Custom Surface-Hopping Scheme

Use scheme=custom only when none of the four named schemes represents the intended calculation. All four low-level choices are then required:

Keyword	Meaning	Allowed values
tdc	time-derivative coupling used to propagate electronic amplitudes	fd, npi, analytic, baeck_an
rescale	direction used to adjust nuclear velocity after an allowed hop	auto, isotropic, analytic_nac, hop_analytic_nac
thrshe	maximum energy gap for a hop attempt, in Hartree	positive number
frustrated	treatment of a directional hop with insufficient kinetic energy	none, reflect

The four named schemes expand as follows:

scheme	tdc	rescale	thrshe	frustrated
BaeckAn	baeck_an	isotropic	0.015936	none
Overlap	npi	isotropic	0.015936	none
TDC_NAC	npi	hop_analytic_nac	0.367493	reflect
NAC	analytic	analytic_nac	0.367493	reflect

Do not combine a named scheme with any of the four low-level keywords. A custom scheme must state all four explicitly:

namd(S1,scheme=custom,tdc=npi,rescale=isotropic,
     thrshe=0.367493,frustrated=reflect)
md(nstep=400,dt=0.5,velocity="molecule.vel")

QM/MM NAMD supports TDC_NAC and NAC for a QM region without link atoms, using the documented frozen-embedding-field QM-region NAC approximation. SOC-NAMD remains experimental and is provided for method development and numerical verification. It requires a defined overlap/isotropic custom scheme, for example:

namd(scheme=custom,tdc=npi,rescale=isotropic,
     thrshe=0.367493,frustrated=reflect,
     soc=true,soc_basis=mch,init_state=S1)
md(nstep=400,dt=0.5)

Diagnostic and Numerical Controls

Purpose	Keywords and defaults
Decoherence parameter	decoherence=edc, edc_c=0.1 Ha
Baeck--An or analytic-NACME comparison	nacme_check=off, ba_gap_max=0.0734986443513 Ha, nacme_policy=off
NACME comparison criteria	nacme_policy_invariant_tol=1.0e-10, nacme_policy_abs_tol=1.0e-4 au⁻¹, nacme_policy_rel_tol=1.0, nacme_policy_consecutive=3
NVE energy criteria	nve_policy_abs_tol=5.0e-3 Ha, nve_policy_step_tol=1.0e-3 Ha, nve_policy_transition_tol=1.0e-6 Ha, nve_policy_consecutive=3
Delayed hopping or trivial-crossing following	first_hop_step=1, trivial=False, trivial_thresh=0.5
Electronic propagation resolution	substep=50000

Use nacme_policy=warn or nve_policy=warn to print the corresponding diagnostic result without terminating the trajectory. Use error only after the relevant numerical thresholds have been established for the molecular system and timestep.

Electronic-Structure Continuity

Use the default continuity=on for the complete analytic-NAC cases A--D treatment. The physical origins, termination behavior, thresholds, and every manual control are documented on NAMD Numerical Continuity. Do not copy an isolated continuity option from an old input; select continuity=manual and report the complete changed set.

Output, Restart, and Continuation

Purpose	Keywords and defaults
Packed trajectory output	trajectory_interval=1; trajectory_file derived from the project name
Atomic checkpoint	restart_interval=10; restart_file derived from the project name
Restart the same calculation	restart=False; normally run the generated .namd.restart.oqp file
Continue into new output files	continuation_checkpoint, continuation_trajectory empty by default

Local continuation with a changed timestep is restricted to fixed-step, same-spin NAC dynamics. The new timestep cannot exceed the timestep stored in the source checkpoint.

NVT and SOC-Specific Controls

Purpose	Keywords and defaults
Langevin NVT	md(ensemble=nvt,temperature=300.0,friction=1.0)
SOC initial MCH character	init_state empty by default
SOC force diagnostics	soc_du_dt_corr=False, soc_tdc_grad_corr=False, grad_wthr=0.001
Adaptive SOC timestep	dt_adaptive=False, dt_min=0.05 fs, dx_max=0.02 bohr

With the default velocity=maxwell, OpenQP samples initial velocities at temperature=300.0 K even for NVE dynamics. temperature does not alter a velocity read from a file or set to zero; with ensemble=nvt, the same value is the NVT target. The sectioned .inp compatibility names are init_temp, thermostat_temperature, and thermostat_friction.

Detailed Definitions

The complete definitions are separated by purpose: coupling schemes, numerical continuity, diagnostics, initial conditions and restart, and ensembles and SOC-NAMD. This page is the short index for deciding whether an advanced control is needed.

Internal Concise-Input Markers

common_controls and common_control_keys are generated internally when OpenQP lowers a concise md(...) call to the sectioned runtime configuration. They preserve which common nuclear controls were written by the user and are not user-facing scientific options. Do not place either keyword in a hand-written input.