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Monte Carlo molecular modeling

About: Monte Carlo molecular modeling is a research topic. Over the lifetime, 11307 publications have been published within this topic receiving 409122 citations.


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Journal ArticleDOI
TL;DR: In this article, a simple and stable method for computing accurate expectation values of observables with variational Monte Carlo or diffusion Monte Carlo (DMC) algorithms is presented, which consists in replacing the usual "bare" estimator associated with the observable by an improved or normalized estimator.
Abstract: A simple and stable method for computing accurate expectation values of observables with variational Monte Carlo (VMC) or diffusion Monte Carlo (DMC) algorithms is presented. The basic idea consists in replacing the usual “bare” estimator associated with the observable by an improved or “renormalized” estimator. Using this estimator more accurate averages are obtained: Not only the statistical fluctuations are reduced but also the systematic error (bias) associated with the approximate VMC or (fixed-node) DMC probability densities. It is shown that improved estimators obey a zero-variance zero-bias property similar to the usual zero-variance zero-bias property of the energy with the local energy as improved estimator. Using this property improved estimators can be optimized and the resulting accuracy on expectation values may reach the remarkable accuracy obtained for total energies. As an important example, we present the application of our formalism to the computation of forces in molecular systems. Cal...

123 citations

Journal ArticleDOI
TL;DR: A kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes, is presented.
Abstract: We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes. A rule identifies the molecular components involved in a transformation, how these components change, conditions that affect whether a transformation occurs, and a rate law. The computational cost of the method, unlike conventional simulation approaches, is independent of the number of possible reactions, which need not be specified in advance or explicitly generated in a simulation. To demonstrate the method, we apply it to study the kinetics of multivalent ligand-receptor interactions. We expect the method will be useful for studying cellular signaling systems and other physical systems involving aggregation phenomena.

123 citations

Journal ArticleDOI
TL;DR: In this article, a new Monte Carlo method for calculating the surface tension of a liquid is described, based on a direct evaluation of the free energy required to create a surface, unlike earlier Monte Carlo calculations which evaluated the surface stress.
Abstract: A new Monte Carlo method for calculating the surface tension of a liquid is described. The method is based on a direct evaluation of the free energy required to create a surface, unlike earlier Monte Carlo calculations which evaluated the surface stress. It is applied to the 6:12 fluid in conditions close to the triple point for argon. The calculated surface tension agrees within statistical uncertainty with previous Monte Carlo estimates, but the statistical uncertainty of the present method is much lower. Agreement with experimental data for argon is not good, as should be expected; estimates of the effects of using a correct pair potential and particularly of including three‐body interactions indicate that they would lead to good agreement.

123 citations

Journal ArticleDOI
TL;DR: In this paper, a new pressure coupling method is described that combines Monte Carlo volume-space sampling with traditional molecular dynamics calculations to simulate the physical properties of molecular systems under standard conditions, where the pressure is maintained by accepting or rejecting volume moves of newly propagated configurations using the Metropolis algorithm with probability P(ΔV) = min (1, exp (( −1 kT 0 ){ΔE + P 0 ΔV − NkT 0 ln [ (V + ΔV) V ]})).

122 citations

Journal ArticleDOI
TL;DR: In this paper, an extended version of the 3D Monte Carlo edge plasma transport code EMC3 including more complex physics is presented, and the balance equations for mass, momentum and energies are formulated in a general conservation form suited for direct application of the Monte Carlo solving algorithm.

122 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202313
202242
20212
20203
20198
201853