Protein folding and protein–ligand docking have long persisted as important subjects in
biophysics. Using multicanonical molecular dynamics (McMD) simulations with realistic …

We present a powerful replica exchange method, particularly suited to first-order phase
transitions associated with the backbending in the statistical temperature, by merging an …

We present a modification of the Rose-Machta algorithm [N. Rose and J. Machta, Phys. Rev.
E 100, 063304 (2019) 2470-0045 10.1103/PhysRevE. 100.063304] and estimate the density …

The development of new algorithms for simulations in physics is as important as the
development of new analytical methods. In this paper, we present a comparison of the …

Chitosan is an important biopolymer in the medical applications because of its excellent
biocompatibility. It has been recently highlighted in the targeted drug delivery system (DDS) …

The replica exchange statistical temperature molecular dynamics (RESTMD) algorithm is
presented, designed to alleviate an extensive increase of the number of replicas required as …

A framework is presented for carrying out simulations of equilibrium systems in the
microcanonical ensemble using annealing in an energy ceiling. The framework …

We propose a scheme for replica exchange molecular dynamics of proteins in explicit
solvent that minimizes the number of required replicas using velocity rescaling. Our …

While the use of replica-exchange molecular dynamics in protein simulations has become
ubiquitous, its utility is limited in many practical applications. We propose to overcome some …

An implementation of the replica exchange with dynamical scaling (REDS) method in the
commonly used molecular dynamics program GROMACS is presented. REDS is a replica …