9 papers · 1 filter
Multicanonical Algorithm, Simulated Tempering, Replica-Exchange Method, and All That
Ayori Mitsutake, Yuko Okamoto
We discuss multi-dimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function $E_…
Thermodynamics of two lattice ice models in three dimensions
Chizuru Muguruma, Yuko Okamoto, Bernd A. Berg
In a recent paper we introduced two Potts-like models in three dimensions, which share the following properties: (A) One of the ice rules is always fulfilled (in particular also at…
Explicit Symplectic Integrators of Molecular Dynamics Algorithms for Rigid-Body Molecules in the Canonical, Isothermal-Isobaric, and Related Ensembles
Hisashi Okumura, Satoru G. Itoh, Yuko Okamoto
We propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isothermal-isobaric ensembles. We also present a symp…
Effective Sampling in the Configurational Space by the Multicanonical-Multioverlap Algorithm
Satoru G. Itoh, Yuko Okamoto
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…
Prediction of transmembrane helix configurations by replica-exchange simulations
Hironori Kokubo, Yuko Okamoto
We propose a method for predicting helical membrane protein structures by computer simulations. Our method consists of two parts. In the first part, amino-acid sequences of the tra…
Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory
Giovanni La Penna, Ayori Mitsutake, Masato Masuya +1
Generalized-ensemble algorithm and diffusion theory have been combined in order to compute the dynamical properties monitored by nuclear magnetic resonance experiments from efficie…