2 citations · 4 across the 4 of their papers we have counts for
4 papers
Free energy calculations of a proton transfer reaction by simulated tempering umbrella sampling first principles molecular dynamics simulations
Yoshiharu Mori, Yuko Okamoto
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles…
Enhanced Sampling Algorithms
Ayori Mitsutake, Yoshiharu Mori, Yuko Okamoto
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-en…
Generalized-Ensemble Algorithms for the Isobaric-Isothermal Ensemble
Yoshiharu Mori, Yuko Okamoto
We present generalized-ensemble algorithms for isobaric-isothermal molecular simulations. In addition to the multibaric-multithermal algorithm and replica-exchange method for the i…
Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms
Yoshiharu Mori, Yuko Okamoto
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of eac…