Computer simulation of liquids
Computer simulation of liquids
The Nosé-Poincaré method for constant temperature molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Backward Error Analysis for Numerical Integrators
SIAM Journal on Numerical Analysis
Understanding Molecular Simulation
Understanding Molecular Simulation
Monitoring energy drift with shadow Hamiltonians
Journal of Computational Physics
What Makes Molecular Dynamics Work?
SIAM Journal on Scientific Computing
On the estimation and correction of discretization error in molecular dynamics averages
Applied Numerical Mathematics
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We investigate the influence of numerical discretization errors on computed averages in a molecular dynamics simulation of TIP4P liquid water at 300K coupled to different deterministic (Nose-Hoover and Nose-Poincare) and stochastic (Langevin) thermostats. We propose a couple of simple practical approaches to estimating such errors and taking them into account when computing the averages. We show that it is possible to obtain accurate measurements of various system quantities using step sizes of up to 70% of the stability threshold of the integrator, which for the system of TIP4P liquid water at 300K corresponds to the step size of about 7fs.