Skip to search formSkip to main contentSkip to account menu
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen's Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The…
View on Wiley
Multidimensional free‐energy calculations using the weighted histogram analysis method
TLDR
The recently formulated WHAM method is an extension of Ferrenberg and Swendsen's multiple histogram technique for free‐energy and potential of mean force calculations and provides an analysis of the statistical accuracy of the potential ofmean force as well as a guide to the most efficient use of additional simulations to minimize errors.
View on Wiley
Feeling textures through a probe: Effects of probe and surface geometry and exploratory factors
TLDR
Log magnitude was consistently a quadratic function of log spacing between elements in the surface and the location of the function’s peak was related to the drop point—that is, the spacing at which the probe can just drop between elements—which was affected by probe tip diameter, element height, and speed.
View on Springer
Magnetic ground state of semiconducting transition-metal trichalcogenide monolayers
Layered transition-metal trichalcogenides with the chemical formula $AB{X}_{3}$ have attracted recent interest as potential candidates for two-dimensional magnets. Using first-principles calculations…
View PDF on arXiv
Monte Carlo renormalization group
Monte Carlo computer simulations have long been used to obtain information on the behavior of thermodynamic systems. The method has the advantages of being applicable to a very large class of models…
View on Springer
Statistical Mechanics of Classical Systems with Distinguishable Particles
The properties of classical models of distinguishable particles are shown to be identical to those of a corresponding system of indistinguishable particles without the need for ad hoc corrections. An…
View on Springer
Dynamics of random sequential adsorption
View via Publisher
Negative temperatures and the definition of entropy
View PDF on arXiv
Comparison of free energy methods for molecular systems.
TLDR
The results demonstrate that the adaptive integration approach is the best overall method for the systems studied here, and the single-ensemble path sampling approach is found to be superior to ordinary Jarzynski averaging for the unidirectional, "fast-growth" nonequilibrium case.
View on PubMed
Transition Matrix Monte Carlo Method
We present a formalism of the transition matrix Monte Carlo method. A stochastic matrix in the space of energy can be estimated from Monte Carlo simulation. This matrix is used to compute the density…
View on Springer
...
...
By clicking accept or continuing to use the site, you agree to the terms outlined in our Privacy Policy, Terms of Service, and Dataset License