829 citations · 1.1k across the 5 of their papers we have counts for
5 papers
Generalized-ensemble simulations of spin systems and protein systems
T. Nagasima, Y. Sugita, A. Mitsutake +1
In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the gen…
Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms
Y. Sugita, Y. Okamoto
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchan…
Generalized-Ensemble Algorithms for Molecular Simulations of Biopolymers
Ayori Mitsutake, Yuji Sugita, Yuko Okamoto
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical en…
Multidimensional replica-exchange method for free-energy calculations
Yuji Sugita, Akio Kitao, Yuko Okamoto
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with d…
Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
Yuji Sugita, Yuko Okamoto
We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical w…