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Molecular dynamics simulations require barostats to be performed at constant pressure. The usual recipe is to employ the Berendsen barostat first, which displays a first-order volume relaxation efficient in equilibration but results in incorrect volume fluctuations, followed by a second order or Monte Carlo barostat for production runs. In this paper, we introduce stochastic cell rescaling, a first-order barostat that samples the correct volume fluctuations by including a suitable noise term. The algorithm is shown to report volume fluctuations compatible with the isobaric ensemble and its anisotropic variant is tested on a membrane simulation. Stochastic cell rescaling can be straightforwardly implemented in existing codes and can be used effectively both in equilibration and in production phases.
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case, however, that th
Kinetic energy equipartition is a premise for many deterministic and stochastic molecular dynamics methods that aim at sampling a canonical ensemble. While this is expected for real systems, discretization errors introduced by the numerical integrati
A powerful control method in experimental quantum computing is the use of spin echoes, employed to select a desired term in the systems internal Hamiltonian, while refocusing others. Here we address a more general problem, describing a method to not
A fundamental question in biology is how cell populations evolve into different subtypes based on homogeneous processes at the single cell level. Here we show that population bimodality can emerge even when biological processes are homogenous at the
We show that a recently introduced stochastic thermostat [J. Chem. Phys. 126 (2007) 014101] can be considered as a global version of the Langevin thermostat. We compare the global scheme and the local one (Langevin) from a formal point of view and th