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Interpretation of atomic motion in flexible molecules: accelerating molecular dynamics simulations
Igor Omelyan1, Andriy Kovalenko
1Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada. omelyan@icmp.lviv.ua
Summary
We developed a new method to separate atomic velocities in flexible molecules, simplifying kinetic energy calculations and enabling longer simulation time steps for molecular dynamics. This approach enhances the study of molecular properties.
Area of Science:
- Computational Chemistry
- Molecular Dynamics
- Statistical Mechanics
Background:
- Standard methods for analyzing molecular motion, like the Eckart method, involve complex Coriolis terms in kinetic energy calculations.
- Previous extensions of molecular dynamics simulations for flexible molecules had limitations on time step size, restricting the study of conformational properties.
Purpose of the Study:
- To introduce a novel approach for partitioning atomic velocities into translational, rotational, and vibrational components.
- To develop a method that simplifies kinetic energy expressions by avoiding the Coriolis contribution.
- To extend microcanonical multiple-time-step dynamics to the canonical-isokinetic Nosé-Hoover chain ensemble for flexible molecules.
Main Methods:
- Decomposing atomic velocities into translational, rotational, and vibrational parts.
- Formulating kinetic energy without the Coriolis term.
- Integrating translational, orientational, and vibrational motion within the Nosé-Hoover chain dynamics.
- Performing molecular dynamics simulations using the flexible TIP3P water model.
Main Results:
- The proposed method simplifies the kinetic energy expression for flexible molecules.
- The new approach allows for the extension to the canonical-isokinetic Nosé-Hoover chain ensemble.
- Molecular dynamics simulations demonstrated the ability to use significantly larger outer time steps (hundreds of femtoseconds to picoseconds).
- Accuracy in studying conformational properties was maintained with extended time steps.
Conclusions:
- The novel velocity partitioning method offers a more straightforward way to calculate kinetic energy for flexible molecules.
- This approach overcomes the time step limitations of previous methods, enabling more efficient and accurate molecular dynamics simulations.
- The enhanced simulation capabilities facilitate the study of molecular conformational properties over longer timescales.
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