METHOD AND SYSTEM FOR MOLECULAR DYNAMICS SIMULATION WITH STABILITY CONTROL

摘要

The present invention is applicable in the field of molecular dynamics, said invention consisting of computing methods for predicting the structure and function of biomolecules, and particularly of proteins, by means of simulating the protein folding process and the interaction process of proteins with other biomolecules in a solvent. More particularly, the invention relates to a method and a system for controlling simulation stability and for choosing the timestep used in the numerical integration of the equations of motion. The invention successfully reduces the molecular dynamics simulation time by means of optimizing the timestep choice through an adaptive control or allowing larger timesteps correcting the trajectories based on a power control.

主权项

1. Computer-implemented method for simulating systems of atoms by means of molecular dynamics, comprising:
using at least one numerical integrator for integrating the equations of motion of the atoms of said system, controlling the power of at least part of the atoms of the system to be simulated, adaptively modifying the timestep value of said numerical integrator, maintaining power within a stability range of power within which the simulation of the system is considered stable, and integrating the equations of motion of the atoms by means of said computer at the rate marked by the timestep chosen for the integrator, maintaining the simulation stable as a result of the power control.