[odp]

The [odp] section adds one one-dimensional-projection (ODP) umbrella window to nonadiabatic dynamics (runtype=namd, namd(...) in .oqp) or to ground-state QM/MM molecular dynamics (md(...) with qmmm(...)). Several windows sampled this way are combined into a potential of mean force with WHAM; see the ODP umbrella sampling workflow.

ODP runs in all-QM NAMD, in QM/MM NAMD and in ground-state QM/MM MD, in the NVE ensemble or the Langevin NVT ensemble, and in nonperiodic or periodic (orthorhombic cutoff=PME) QM/MM. It is not available with SOC-NAMD (soc=true), with all-QM ground-state MD, or with other runtypes.

odp(enabled=true,cv="distance(1,2);asymmetric_distance(1,3,1,4);angle(3,1,4)",scale="0.5,0.5,1.0",reference_r="2.10,-0.10,1.90",reference_p="2.50,0.10,2.20",center=0.5,k_parallel=0.02,k_perpendicular=0.005,window=1)

Bias

Each collective variable q_i (CV) is mapped to the dimensionless coordinate X_i = scale_i q_i. With the reactant and product references R and P in the same scaled space

d     = scale * (reference_p - reference_r)          path direction
u     = scale * q - scale * reference_r              displacement from R
xi    = (u . d) / (d . d)                            0 at R, 1 at P
u_perp = u - xi d
V     = 1/2 k_parallel (xi - center)^2 + 1/2 k_perpendicular |u_perp|^2

The atomic force is the exact derivative of V. V is added to the potential energy, so it is part of the conserved energy in NVE and of the energy balance in NVT.

In a periodic QM/MM cell every CV takes its own minimum-image value: each atom pair a CV uses (the two atoms of a distance, both pairs of an asymmetric distance, and both arms of an angle from its vertex) is taken at its minimum-image separation, independently of the other CVs. CVs whose pairs form a ring around the cell are therefore measured correctly as well. The run stops only when a pair is exactly half the box length apart along an axis, where the minimum image is not unique.

Keywords

enabled

Field	Value
Type	boolean
Default	False
Used by	runtype=namd; runtype=md with QM/MM

Turns the umbrella window on.

cv

Field	Value
Type	string
Default	none (required)
Indexing	1-based; in QM/MM, indices of the full QM+MM system

Semicolon-separated CVs: distance(a,b) (bohr), asymmetric_distance(a,b,c,d) = d(a,b) - d(c,d) (bohr), and angle(a,b,c) with vertex b (radian).

scale

Field	Value
Type	float list, one positive value per CV
Default	none (required)
Units	1/bohr for distances, 1/radian for angles

Converts each CV into the dimensionless coordinate used by the projection.

reference_r, reference_p

Field	Value
Type	float list, one value per CV
Default	none (required)
Units	bohr or radian, as the CV

Reactant and product values of the CVs. The scaled references must differ.

center

Field	Value
Type	float
Default	0.0

Target value of xi for this window (0 at the reactant, 1 at the product).

k_parallel

Field	Value
Type	float
Default	none (required, positive)
Units	Hartree

Force constant along xi.

k_perpendicular

Field	Value
Type	float
Default	0.0 (no perpendicular restraint)
Units	Hartree

Force constant on the scaled displacement perpendicular to the path.

window

Field	Value
Type	integer
Default	0

Non-negative label of the window. It is written to every trajectory record and used by WHAM to group the samples of one window.

Output

The packed NAMD trajectory (<project>.namd.trj) stores the window definition in its header (odp) and, for every step, odp_window, odp_xi, the raw, scaled, and perpendicular CVs, and the parallel, perpendicular, and total bias (odp_bias_hartree). The header also records the ensemble and, for NVT, the thermostat temperature that WHAM checks.

Ground-state QM/MM MD writes the same per-step records into its energy table (total_energy.npz), next to the unbiased potential (E_unbiased, e_unbiased_pot_hartree) and the droplet and solute_com restraint energies. The table stores the window definition, the ensemble, the thermostat temperature and an identity of the system as bias_metadata_json: topology and QM region; every QM option that changes the surface (method, basis with file-backed basis sets by content, library, ispher, scf, dftgrid, ...); the contents of the force-field files and of every file they include, with the QM/MM Hamiltonian options; the ESPF_* environment controls; the contents of DFTB/xTB parameter and backend files; the frozen atoms and constraints; and, for PME, the cell. WHAM reads these tables like packed NAMD trajectories and refuses to combine windows whose identities differ.