Integrator Reference
Time integration algorithms for propagating the equations of motion. NeuroCGMD implements velocity-Verlet and BAOAB Langevin integrators with stochastic thermostats for canonical (NVT) sampling.
▶ VELOCITY-VERLET LANGEVIN — primary integrator for production dynamics
Velocity-Verlet Langevin
Primary integrator — two force evaluations per step
The workhorse integrator for production dynamics. Implements the velocity-Verlet algorithm with an optional Langevin thermostat for NVT sampling.
Algorithm (per timestep):
The thermostat (step 2) is only applied when
Kinetic energy is computed at each step: Ek = ½ ∑ mi |vi|²
Algorithm (per timestep):
1. vn+½ = vn + (Δt/2m) Fn
2. Apply thermostat: vdamped = e−γΔt v + √((1−e−2γΔt) kT/m) · ξ
3. xn+1 = xn + Δt · vn+½
4. Evaluate Fn+1 at new positions
5. vn+1 = vn+½ + (Δt/2m) Fn+1
The thermostat (step 2) is only applied when
stochastic=True. The noise term ξ is drawn from a standard normal distribution, ensuring correct Boltzmann sampling at the target temperature.Kinetic energy is computed at each step: Ek = ½ ∑ mi |vi|²
alternative integrator
▶ BAOAB LANGEVIN SPLITTING — symmetric splitting, one force eval per step
BAOAB Langevin Splitting
Symmetric splitting — one force evaluation per step
An alternative integrator based on the BAOAB splitting scheme (Leimkuhler & Matthews, 2013). Splits the Liouvillian into kick (B), drift (A), and Ornstein-Uhlenbeck (O) substeps in the symmetric pattern B-A-O-A-B.
Advantages: better configurational sampling accuracy for equivalent timestep; only one force evaluation per step (vs two for velocity-Verlet). Commonly used in enhanced sampling applications.
Advantages: better configurational sampling accuracy for equivalent timestep; only one force evaluation per step (vs two for velocity-Verlet). Commonly used in enhanced sampling applications.
parameters
▶ PARAMETERS — click to expand details
time_step
Default: 0.02 ps
Integration timestep. For CG dynamics, timesteps of 0.01–0.04 ps are typical. Stability depends on the fastest vibrational mode (bond frequency).
friction_coefficient
Default: from state
Langevin coupling constant γ (ps−1). Controls the strength of thermostat coupling. Higher values: stronger coupling, faster equilibration. Lower values: more natural dynamics.
stochastic
Default: False
Enable the stochastic Langevin noise term. Required for NVT sampling. When False, the integrator runs as deterministic velocity-Verlet (NVE-like).
thermal_energy_scale
Default: 1.0
Scaling factor for kT in the noise term. Normally 1.0 for standard simulations. Can be adjusted for replica exchange or simulated tempering protocols.