Related papers: Multidimensional replica-exchange method for free-…
A method to generate reactive trajectories, namely equilibrium trajectories leaving a metastable state and ending in another one is proposed. The algorithm is based on simulating in parallel many copies of the system, and selecting the…
A new formulation of the stochastic potential switching algorithm is presented. This reformulation naturally leads us to a generalized Fourtuin-Kasteleyn representation of the partition function Z. A formula for internal energy E and that…
We present a new method to compute free energies at a quantum mechanical (QM) level of theory from molecular simulations using cheap reference potential energy functions, such as force fields. To overcome the poor overlap between the…
Parallel tempering, also known as replica exchange sampling, is an important method for simulating complex systems. In this algorithm simulations are conducted in parallel at a series of temperatures, and the key feature of the algorithm is…
A new method of accessing information on the symmetry free energy from yields of fragments produced in Fermi-energy heavy-ion collisions is proposed. Furthermore, by means of quantum fluctuation analysis techniques, correlations between…
This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration. We employ linear regression to construct a polynomial that optimally fits the thermodynamic integration…
We propose a new method to compute the free energy or enthalpy of fluids or disordered solids by computer simulation . The main idea is to construct a reference system by freezing one representative configuration, and then carry out a…
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…
Exploring the free-energy landscape along reaction coordinates or system parameters $\lambda$ is central to many studies of high-dimensional model systems in physics, e.g. large molecules or spin glasses. In simulations this usually…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
An analytic method for deriving the free energy of a three-dimensional Ising-like system near the critical point in a homogeneous external field is developed in the $\rho^6$ model approximation. The mathematical description proposed for…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and…
We discuss resummation strategies for free energy in quantum field theories at nonzero temperatures T. We point out that resummations should be performed for the short- and long-distance parts separately in order to avoid spurious…
We propose an algorithm for molecular dynamics or Monte Carlo simulations that uses an interpolation procedure to estimate potential energy values from energies and gradients evaluated previously at points of a simplicial mesh. We chose an…
We introduce a new model and mechanism of high temperature pairing in stripes. We propose a way to unambiguously test it by numerical simulations. For example, the implementation of our mechanism in a 6-leg t-J ladder model has the effect…
Markov chain Monte Carlo methods are primarily used for sampling from a given probability distribution and estimating multi-dimensional integrals based on the information contained in the generated samples. Whenever it is possible, more…
Replica exchange (RE) is one of the most popular enhanced-sampling simulations technique in use today. Despite widespread successes, RE simulations can sometimes fail to converge in practical amounts of time, e.g., when sampling around…
A systematic replica field theory calculations are analysed using the examples of two particular one-dimensional "toy" random models with Gaussian disorder. Due to apparent simplicity of the model the replica trick calculations can be…
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…