From predictors and SHAKE toward unified integration scheme for molecular dynamics

Area of Science:

• Computational physics and chemistry
• Molecular dynamics simulations
• Numerical integration methods

Background:

• Specialized tasks in molecular dynamics (MD) simulations often necessitate custom integration algorithms.
• This complexity complicates the development and maintenance of MD simulation software.

Purpose of the Study:

• To propose a unified integration scheme for solving common equations of motion in MD simulations.
• To simplify the development of new integrators and the maintenance of existing MD software.

Main Methods:

• Adapted the SHAKE method for rigid bonds into a predictor-corrector scheme.
• Combined this with time-reversible velocity and box predictors.
• Integrated with Verlet and Gear methods for various ensembles (microcanonical, canonical, isobaric).

Main Results:

• Successfully tested on simple models, SPC/E water, and ionic liquid systems.
• Generated trajectories in microcanonical, Nosé-Hoover canonical, and MTK isobaric ensembles.
• Verlet-based methods showed excellent agreement with conventional approaches.

Conclusions:

• The unified scheme offers a simpler approach to developing and maintaining MD simulation software.
• The new integrators are suitable for massively parallel MD software.
• This approach facilitates the implementation of specialized MD simulation tasks.