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We present a reversible and symplectic algorithm called ROLL, for integrating the equations of motion in molecular dynamics simulations of simple fluids on a hypersphere $mathcal{S}^d$ of arbitrary dimension $d$. It is derived in the framework of geometric algebra and shown to be mathematically equivalent to algorithm RATTLE. An application to molecular dynamics simulation of the one component plasma is briefly discussed.
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leave
Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in molecular mod
This paper had no abstract originally. A second-order symplectic integration algorithm for guiding center motion is presented. The algorithm is based on the Poincare (mid-point) generating function.
To take into account nuclear quantum effects on the dynamics of atoms, the path integral molecular dynamics (PIMD) method used since 1980s is based on the formalism developed by R. P. Feynman. However, the huge computation time required for the PIMD
Kinetic energy equipartition is a premise for many deterministic and stochastic molecular dynamics methods that aim at sampling a canonical ensemble. While this is expected for real systems, discretization errors introduced by the numerical integrati