Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats
This work provides practical guidelines for choosing step sizes in molecular dynamics simulations, benefiting researchers in computational chemistry and biophysics.
The authors investigate discretization errors in molecular dynamics simulations of TIP4P water with various thermostats, proposing practical methods to estimate and account for these errors. They achieve accurate measurements using step sizes up to 70% of the stability threshold (about 7 fs).
We investigate the influence of numerical discretization errors on computed averages in a molecular dynamics simulation of TIP4P liquid water at 300 K coupled to different deterministic (Nosé-Hoover and Nosé-Poincaré) 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 300 K corresponds to the step size of about 7 fs.