Related papers: Adaptively Biased Molecular Dynamics for Free Ener…
A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schroedinger-like…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
We present a combination of the recently developed double incremental expansion of potential energy surfaces with the well-established adaptive density-guided approach to grid construction. This unique methodology is based on the use of an…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
We propose a method to compute free-energy differences from nonadiabatic alchemical transformations using flow-based generative models. The method, nonadiabatic force matching, hinges on estimating the dissipation along an alchemical…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
Enhanced sampling methods such as metadynamics and umbrella sampling have become essential tools for exploring the configuration space of molecules and materials. At the same time, they have long faced a number of issues such as the…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
Energy-based models (EBMs) provide a powerful and flexible way of learning a joint probability distribution over data by constructing an energy surface. This energy surface enables insight extraction and conditional sampling. We apply EBMs…
We propose a methodology for fully automated calculation of thermal rate coefficients of gas phase chemical reactions, which is based on combining the ring polymer molecular dynamics (RPMD) with the machine-learning interatomic potentials…
We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem…
The paper develops a method for the numerical simulation of a free-surface flow of incompressible viscous fluid around a streamlined body. The body is a rigid stationary construction partially submerged in the fluid. The application we are…
We present an efficient method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram…
ADBSat is a novel software that determines the aerodynamic properties of any body in free-molecular flow. Its main advantage is the fast approximation of the aerodynamics of spacecraft in the lower end of the low-Earth orbit altitude range.…