ﻻ يوجد ملخص باللغة العربية
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 temperature-update and pressure-update are self-updated independently according to the trapezoidal rule. In order to test the effectiveness of the algorithm, we applied our proposed method to a peptide, chignolin, in explicit water. After setting all weight parameters to zero, the weight parameters were quickly determined during the simulation. The simulation realised a uniform random walk in the entire temperature-pressure space.
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 prop
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamil
We performed two-dimensional simulated tempering (ST) simulations of the two-dimensional Ising model with different lattice sizes in order to investigate the two-dimensional STs applicability to dealing with phase transitions and to study the crossov
Parallel tempering Monte Carlo has proven to be an efficient method in optimization and sampling applications. Having an optimized temperature set enhances the efficiency of the algorithm through more-frequent replica visits to the temperature limits
In the previous paper of this series [JCTC 2020, 16, 3757], we presented a theoretical and algorithmic framework based on a localized representation of the occupied space that exploits the inherent sparsity in the real-space evaluation of the EXX int