odp controls in .oqp¶
.oqp control reference
Use canonical routes and controls in input files. Raw names
identify implementation storage. A control without an accepted canonical
spelling is not available in .oqp files.
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 qi (CV) is mapped to the dimensionless
coordinate Xi = scalei qi. 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¶
Use the physical route or primary calculation for this control; see the canonical spelling and ownership. Do not write this raw storage key as a separate input section.
| Field | Value |
|---|---|
| Type | boolean |
| Default | False |
| Used by | runtype=namd; runtype=md with QM/MM |
Turns the umbrella window on.
cv¶
Use the physical route or primary calculation for this control; see the canonical spelling and ownership. Do not write this raw storage key as a separate input section.
| 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¶
Use the physical route or primary calculation for this control; see the canonical spelling and ownership. Do not write this raw storage key as a separate input section.
| 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¶
Use the physical route or primary calculation for this control; see the canonical spelling and ownership. Do not write this raw storage key as a separate input section.
| Field | Value |
|---|---|
| Type | float |
| Default | 0.0 |
Target value of xi for this window (0 at the reactant, 1 at the product).
k_parallel¶
Use the physical route or primary calculation for this control; see the canonical spelling and ownership. Do not write this raw storage key as a separate input section.
| Field | Value |
|---|---|
| Type | float |
| Default | none (required, positive) |
| Units | Hartree |
Force constant along xi.
k_perpendicular¶
Use the physical route or primary calculation for this control; see the canonical spelling and ownership. Do not write this raw storage key as a separate input section.
| Field | Value |
|---|---|
| Type | float |
| Default | 0.0 (no perpendicular restraint) |
| Units | Hartree |
Force constant on the scaled displacement perpendicular to the path.
window¶
Use the physical route or primary calculation for this control; see the canonical spelling and ownership. Do not write this raw storage key as a separate input section.
| 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.