Related papers: Simulating Met-Enkephalin With Population Annealin…
Population annealing is a powerful tool for large-scale Monte Carlo simulations. We adapt this method to molecular dynamics simulations and demonstrate its excellent accelerating effect by simulating the folding of a short peptide commonly…
We compare a few variants of the recently proposed multicanonical method with the well known simulated annealing for the effectiveness in search of the energy global minimum of a biomolecular system. For this we study in detail…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
We compare numerically the effectiveness of three recently proposed algorithms, multicanonical simulations, simulations in a 1/k-ensemble, and simulated tempering for the protein folding problem. For this we perform simulations with high…
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…
Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of…
We propose a new generalized-ensemble algorithm, which we refer to as the multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the multi-dimensional, energy-overlap space…
Population Monte Carlo simulations in the form commonly referred to as population annealing can serve as a useful meta-algorithm for simulating systems with complex free-energy landscapes. In the present paper we provide an easily…
A modified version of stochastic tunneling, a recently introduced global optimization technique, is introduced as a new generalized-ensemble technique and tested for a benchmark peptide, Met-enkephalin. It is demonstrated that the new…
We apply a recently developed method, multicanonical algorithm, to the problem of tertiary structure prediction of peptides and proteins. As a simple example to test the effectiveness of the algorithm, Met-enkephalin is studied and the…
We test the effectiveness of the multicanonical algorithm for the tertiary structure prediction of peptides and proteins. As a simple example we study Met-enkephalin. The lowest-energy conformation obtained agrees with that determined by…
We study the free energy landscape of the small peptide Met-enkephalin. Our data were obtained from a generalized-ensemble Monte Carlo simulation taking the interactions among all atoms into account. We show that the free energy landscape…
We investigate the solvent-accessible area method by means of Metropolis simulations of the brain peptide Met-Enkephalin at 300$ K$. For the energy function ECEPP/2 nine atomic solvation parameter (ASP) sets are studied. The simulations are…
We demonstrate that the multicanonical approach is not restricted to Monte Carlo simulations, but can also be applied to simulation techniques such as molecular dynamics, Langevin, and hybrid Monte Carlo algorithms. The effectiveness of the…
The charge transfer and polarization effects are important components in the molecular mechanism description of bio-molecules. Classical force field with fixed point charge cannot take into the account of the non-negligible correlation…
Population annealing is an efficient sequential Monte Carlo algorithm for simulating equilibrium states of systems with rough free energy landscapes. The theory of population annealing is presented, and systematic and statistical errors are…
Population annealing is a sequential Monte Carlo scheme well-suited to simulating equilibrium states of systems with rough free energy landscapes. Here we use population annealing to study a binary mixture of hard spheres. Population…
We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the…
We previously developed an algorithm, called resolution exchange, which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations[1]. Here, we demonstrate a generally…
Population annealing is an easily parallelizable sequential Monte Carlo algorithm that is well-suited for simulating the equilibrium properties of systems with rough free energy landscapes. In this work we seek to understand and improve the…