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We present generalized-ensemble algorithms for isobaric-isothermal molecular simulations. In addition to the multibaric-multithermal algorithm and replica-exchange method for the isobaric-isothermal ensemble, which have already been proposed, we propose a simulated tempering method for this ensemble. We performed molecular dynamics simulations with these algorithms for an alanine dipeptide system in explicit water molecules to test the effectiveness of the algorithms. We found that these generalized-ensemble algorithms are all useful for conformational sampling of biomolecular systems in the isobaric-isothermal ensemble.
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-exchange method; the latter is also referred to as parallel tempering. We pr
In this work, we show that the dissipation in a many-body system under an arbitrary non-equilibrium process is related to the R{e}nyi divergences between two states along the forward and reversed dynamics under very general family of initial conditio
The local physical properties of an isolated quantum statistical system in the stationary state reached long after a quench are generically described by the Gibbs ensemble, which involves only its Hamiltonian and the temperature as a parameter. If th
We propose a method to extend the fast on-the-fly weight determination scheme for simulated tempering to two-dimensional space including not only temperature but also pressure. During the simulated tempering simulation, weight parameters for temperat
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 symplectic algorithm in the constant normal pressure and lateral surface a