18.8k citations · 35.1k across the 68 of their papers we have counts for
17 papers · 1 filter
Pressure control using stochastic cell rescaling
Mattia Bernetti, Giovanni Bussi
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 volu…
Towards empirical force fields that match experimental observables
Thorben Fröhlking, Mattia Bernetti, Nicola Calonaci +1
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However,…
Analyzing and biasing simulations with PLUMED
Giovanni Bussi, Gareth A. Tribello
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of…
The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models
Giovanni Pinamonti, Fabian Paul, Frank Noé +2
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and M…
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments
Andrea Cesari, Sabine Reißer, Giovanni Bussi
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate fo…
Predicting the kinetics of RNA oligonucleotides using Markov state models
Giovanni Pinamonti, Jianbo Zhao, David E. Condon +4
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obta…
Combining simulations and solution experiments as a paradigm for RNA force field refinement
Andrea Cesari, Alejandro Gil-Ley, Giovanni Bussi
Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA o…
Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering
Alejandro Gil-Ley, Giovanni Bussi
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce…
Accurate multiple time step in biased molecular simulations
Marco Jacopo Ferrarotti, Sandro Bottaro, Andrea Pérez-Villa +1
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of…
PLUMED 2: New feathers for an old bird
Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi +2
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popul…
Hamiltonian replica-exchange in GROMACS: a flexible implementation
Giovanni Bussi
A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different…
Colored-noise thermostats à la carte
Michele Ceriotti, Giovanni Bussi, Michele Parrinello
Recently, we have shown how a colored-noise Langevin equation can be used in the context of molecular dynamics as a tool to obtain dynamical trajectories whose properties are tailo…
PLUMED: a portable plugin for free-energy calculations with molecular dynamics
M. Bonomi, D. Branduardi, G. Bussi +8
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecul…
A simple asynchronous replica-exchange implementation
Giovanni Bussi
We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous…
Conjugate gradient heatbath for ill-conditioned actions
Michele Ceriotti, Giovanni Bussi, Michele Parrinello
We present a method for performing sampling from a Boltzmann distribution of an ill-conditioned quadratic action. This method is based on heatbath thermalization along a set of con…
Stochastic thermostats: comparison of local and global schemes
Giovanni Bussi, Michele Parrinello
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…
Accurate sampling using Langevin dynamics
Giovanni Bussi, Michele Parrinello
We show how to derive a simple integrator for the Langevin equation and illustrate how it is possible to check the accuracy of the obtained distribution on the fly, using the conce…