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Register a new userRandom-batch list algorithm for short-range molecular dynamics simulations
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We propose a fast method for the calculation of short-range interactions in molecular dynamics simulations. The so-called random-batch list method is a stochastic version of the classical neighbor-list method to avoid the construction of a full Verlet list, which introduces two-level neighbor lists for each particle such that the neighboring particles are located in core and shell regions, respectively. Direct interactions are performed in the core region. For the shell zone, we employ a random batch of interacting particles to reduce the number of interaction pairs. The error estimate of the algorithm is provided. We investigate the Lennard-Jones fluid by molecular dynamics simulations, and show that this novel method can significantly accelerate the simulations with a factor of several fold without loss of the accuracy. This method is simple to implement, can be well combined with any linked cell methods to further speed up and scale up the simulation systems, and can be straightforwardly extended to other interactions such as Ewald short-range part, and thus it is promising for large-scale molecular dynamics simulations.
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A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences.
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