Exact and efficient calculation of derivatives of Lagrange multipliers for molecular dynamic simulations of biological molecules

Abstract

In the simulation of biological molecules, it is customary to impose constraints on the fastest degrees of freedom to increase the time step. The evaluation of the involved constraint forces must be performed in an efficient manner, for otherwise it would be a bottleneck in the calculations; for this reason, linearly-scaling calculation methods have become widely used. If integrators of order higher than 2 (e.g. Gear predictor-corrector methods) are used to find the trajectories of atoms, the derivatives of the forces on atoms with respect to the time also need to be calculated, which includes the derivatives of constraint forces. In this letter we prove that such calculation can be analytically performed with linearly scaling numerical complexity (O(Nc), being Nc the number of constraints). This ensures the feasibility of constrained molecular dynamics calculations with high-order integrators.

References in corpus (7)

• A review of High Performance Computing foundations for scientists
• Introduction to protein folding for physicists
• Definition of Systematic, Approximately Separable and Modular Internal Coordinates (SASMIC) for macromolecular simulation
• Exact and efficient calculation of Lagrange multipliers in constrained biological polymers: Proteins and nucleic acids as example cases
• Linearly scaling direct method for accurately inverting sparse banded matrices
• Holonomic constraints : an analytical result
• Ideograms for Physics and Chemistry