Related papers: Infinite swapping replica exchange molecular dynam…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Experiment directed simulation is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics…
We implement a three-body potential to model associative bond swaps, and release it as part of the HOOMD-blue software. The use of a three-body potential to model swaps has been proven to be effective and has recently provided useful…
Two-dimensional Raman and hybrid terahertz/Raman spectroscopic techniques provide invaluable insight into molecular structure and dynamics of condensed-phase systems. However, corroborating experimental results with theory is difficult due…
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates…
Methods to efficiently determine the relative stability of polymorphs of organic crystals are highly desired in crystal structure predictions (CSPs). Current methodologies include use of static lattice phonons, quasi-harmonic approximation…
We introduce and illustrate a number of performance measures for rare-event sampling methods. These measures are designed to be of use in a variety of expanded ensemble techniques including parallel tempering as well as infinite and partial…
We investigate the plasma enhancement of nuclear reactions in the intermediate coupling regime using orbital free molecular dynamics (OFMD) simulations. Mixtures of H-Cu and H-Ag serve as prototypes of simultaneous weak and strong couplings…
Inferential methods can be used to integrate experimental informations and molecular simulations. The maximum entropy principle provides a framework for using equilibrium experimental data and it has been shown that replica-averaged…
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
Small mechanical forces play important functional roles in many crucial cellular processes, including in the dynamical behavior of the cytoskeleton and in the regulation of osmotic pressure through membrane-bound proteins. Molecular…
Although the reverse non-equilibrium molecular dynamics (RNEMD) simulation method has been widely employed, the range of applicability is yet to be discussed. In this study, for the first time, we systematically examine the method against…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
We present a new approach for the two-temperature molecular dynamics (MD) model for coupled simulations of electronic and phonon heat conduction in nanoscale systems. The proposed method uses a master equation to perform heat conduction of…
According to a well-known principle of thermodynamics, the transfer of heat between two bodies is reversible when their temperatures are infinitesimally close. As we demonstrate, a little-known alternative exists: two bodies with…
Enhanced sampling techniques are essential for exploring biomolecular conformational dynamics that occur on timescales inaccessible to conventional molecular dynamics (MD) simulations. This study introduces a framework that combines…
We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different type…
The non-equilibrium process due to irreversible heat exchanges occurring during a temperature modulated differential scanning calorimetry experiment is investigated in detail. This enables us to define an experimental frequency dependent…
Temporal modulation unlocks possibilities to dynamically control and modify the response of electromagnetic systems. Employing explicit dependencies of circuit or surface parameters on time enables the engineering of systems with…