Related papers: Replica-Exchange Method in van der Waals Radius Sp…
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…
A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without…
Van der Waals interactions, as a result of the exchange of photons between particles, can be altered by modifying the environment through which these photons propagate. As a consequence, phenomena such as the Rydberg blockade mechanism…
We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of…
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 have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
This paper presents a matrix formulation of the scalar laws of radiative transfer. The method applies to coupled mixed boundary condition problems on general domains. Participating media can range from transparent to absorbing, emitting,…
A novel overlap histogramming method based on Dual-Topology Hamiltonian-Replica-Exchange simulation technique is presented to efficiently calculate relative free energy difference in rough energy landscape, in which multiple conformers…
We propose a new implementation of the replica-exchange method (REM) in which replicas follow a pre-planned route in temperature space instead of a random walk. Our method satisfies the detailed balance condition in the proposed route. The…
Pauli exchange-repulsion is the dominant short-range intermolecular interaction and it is an essential component of molecular force fields. Current approaches to modeling Pauli repulsion in molecular force fields often rely on over 20 atom…
Because of growing interest in temperature-based sampling methods like replica exchange, this note aims to make some observations and raise some potentially important questions which we have not seen addressed sufficiently in the…
We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM).In RPM not only exchanges…
We propose a replica-exchange method (REM) which does not use pseudo random numbers. For this purpose, we first give a conditional probability for Gibbs sampling replica-exchange method (GSREM) based on the heat bath method. In GSREM,…
We study the phase space structures that control the transport in a classical Hamiltonian model for a chemical reaction. This model has been proposed to study the yield of products in an ultracold exothermic reaction. In the considered…
Within the frame of macroscopic quantum electrodynamics in causal media, the van der Waals interaction between an atomic system and an arbitrary arrangement of dispersing and absorbing dielectric bodies including metals is studied. It is…
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we…
The Random Phase Approximation (RPA) is a widely employed post Hartree-Fock or DFT method, capable of capturing van der Waal interactions and other dynamic correlation effects at relatively low costs of $\mathcal O(N^3)$ in time and…
Using fourth-order perturbation theory, a general formula for the van der Waals potential of two neutral, unpolarized, ground-state atoms in the presence of an arbitrary arrangement of dispersing and absorbing magnetodielectric bodies is…
We verify that the van der Waals interaction and hence all dispersion interactions for the hydrogen molecule given by: W"= -{A/R^6}-{B/R^8}-{C/R^10}- ..., in which R is the internuclear separation, are exactly soluble. The constants…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…