Related papers: O(N) continuous electrostatics solvation energies …
Line-by-line calculations are becoming the standard procedure for carrying spectral simulations. However, it is important to insure the accuracy of such spectral simulations through the choice of adapted models for the simulation of key…
The energy variance extrapolation method consists in relating the approximate energies in many-body calculations to the corresponding energy variances and inferring eigenvalues by extrapolating to zero variance. The method needs a fast…
Accurate prediction of a gas solubility in a liquid is crucial in many areas of chemistry, and a detailed understanding of the molecular mechanism of the gas solvation continues to be an active area of research. Here, we extend the idea of…
We present an energy-specific Bethe-Salpeter equation (BSE) implementation for efficient core and valence optical spectrum calculations. In energy-specific BSE, high-lying excitation energies are obtained by constructing trial vectors and…
We consider systematic numerical approximation of a viscoelastic phase separation model that describes the demixing of a polymer solvent mixture. An unconditionally stable discretisation method is proposed based on a finite element…
In contrast to the gaseous and the solid states, the liquid state does not have a simple model that could be developed into a quantitative theory. A central issue in the understanding of liquids is to estimate the energy state of liquids.…
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Thermostats are dynamical equations used to model thermodynamic variables such as temperature and pressure in molecular simulations. For computationally intensive problems such as the simulation of biomolecules, we propose to average over…
We study alchemical atomic energy partitioning as a method to estimate atomisation energies from atomic contributions which are defined in physically rigorous and general ways through use of the uniform electron gas as a joint reference. We…
A Monte Carlo method is presented to evaluate quantum states with many particles moving in the continuum. The scattering state is generated at each time by a Monte Carlo random sampling algorithm. The same calculation are repeated until the…
Free energy calculations in molecular simulations have a variety of applications including determining the strength of molecular processes such as solvation and binding. It has been recently shown that when removing the VDW and Coulomb…
We present a fast and accurate method to calculate vibrational properties for mechanically unstable high temperature phases that suffer from imaginary frequencies at zero temperature. The method is based on standard finite-difference…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
A family of fast sampling methods is introduced here for molecular simulations of systems having rugged free energy landscapes. The methods represent a generalization of a strategy consisting of adjusting a model for the free energy as a…
Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting…
Electrostatic interactions make a large contribution to solvation free energy in ionic fluids such as electrolytes and colloidal dispersions. The electrostatic contribution to solvation free energy has been ascribed to the self-energy of a…
Using a new analytic quantum mechanical method based on Slater's Xalpha method, we show that a fairly accurate estimate of the total energy of a molecule can be obtained from the exact energies of its constituent atoms. The mean absolute…