GROMACS Stochastic Dynamics and BAOAB are equivalent configurational sampling algorithms
arXiv:2204.02105 · doi:10.1021/acs.jctc.2c00585
Abstract
Two of the most widely used Langevin integrators for molecular dynamics simulations are the GROMACS Stochastic Dynamics (GSD) integrator and the splitting method BAOAB. In this letter, we show that the GROMACS Stochastic Dynamics integrator is equal to the less frequently used splitting method BAOA. It immediately follows that GSD and BAOAB sample the same configurations and have the same high configurational accuracy. Our numerical results indicate that GSD/BAOA has higher kinetic accuracy than BAOAB.
References in corpus (18)
- Accurate sampling using Langevin dynamics
- A simple and effective Verlet-type algorithm for simulating Langevin dynamics
- Robust and efficient configurational molecular sampling via Langevin Dynamics
- Rational Construction of Stochastic Numerical Methods for Molecular Sampling
- A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat
- The computation of averages from equilibrium and nonequilibrium Langevin molecular dynamics
- ATK-ForceField: A New Generation Molecular Dynamics Software Package
- Long-Run Accuracy of Variational Integrators in the Stochastic Context
- Stochastic resonance-free multiple time-step algorithm for molecular dynamics with very large time steps
- Numerical Integration of the Extended Variable Generalized Langevin Equation with a Positive Prony Representable Memory Kernel
- Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems
- Girsanov reweighting for path ensembles and Markov state models
- Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations
- Finite-temperature materials modeling from the quantum nuclei to the hot electrons regime
- Stationary state distribution and efficiency analysis of the Langevin equation via real or virtual dynamics
- Path probability ratios for Langevin dynamics -- exact and approximate
- The role of the dissipative and random forces in the calculation of the pressure of simple fluids with dissipative particle dynamics
- Bringing discrete-time Langevin splitting methods into agreement with thermodynamics