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We evaluate the grand potential of a cluster of two molecular species, equivalent to its free energy of formation from a binary vapour phase, using a nonequilibrium molecular dynamics technique where guide particles, each tethered to a…
A common approach to study nucleation rates is the estimation of free-energy barriers. This usually requires knowledge about the shape of the forming droplet, a task that becomes notoriously difficult in macromolecular setups starting with…
Recent very large molecular dynamics simulations of homogeneous nucleation with $(1-8) \cdot 10^9$ Lennard-Jones atoms [Diemand et al. J. Chem. Phys. {\bf 139}, 074309 (2013)] allow us to accurately determine the formation free energy of…
We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the…
The free energy of glasses cannot be estimated using thermodynamic integration, as glasses are intrinsically not in equilibrium. We present numerical simulations showing that, in contrast, plausible free-energy estimates of a Kob-Andersen…
In thermodynamically characterizing a mixture comprising a finite number of molecules, we consider two kinds of protocol for producing a mixture from a pure substance. The first is a single alchemical operation, whereas the second is a…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
A promising method for calculating free energy differences Delta F is to generate non-equilibrium data via ``fast-growth'' simulations or experiments -- and then use Jarzynski's equality. However, a difficulty with using Jarzynski's…
Using computer simulations, we validate a simple free energy model that can be analytically solved to predict the equilibrium size of self-limiting clusters of particles in the fluid state governed by a combination of short-range attractive…
We perform, with the help of cloud computing resources, extensive Langevin simulations which provide free energy estimates for unbiased three dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
According to the Jarzynski theorem, equilibrium free energy differences can be calculated from the statistics of work carried out during non-equilibrium transformations. Although exact, this approach can be plagued by large statistical…
Despite the strength of Molecular Dynamics simulations in providing insights into the microscopic details of phenomenon in many fields in materials science, physics and biology, the biggest barrier is its limited timescale which is several…
The expression of the free energy of a liquid in terms of an explicit decomposition of the particle configurations into local coordination clusters is examined. We argue that the major contribution to the entropy associated with structural…
In this work the free energy of solid phases is computed for the Lennard-Jones potential and for a model of NaCl. The free energy is evaluated through the Einstein crystal/molecule methodologies using the Molecular Dynamics programs:…
The Jarzynski equality allows the calculation of free-energy differences using values of work measured from nonequilibrium trajectories. The number of trajectories required to accurately estimate free-energy differences in this way grows…
We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n=4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with…
Using a recently developed technique to estimate the equilibrium free energy of glassy materials, we explore if equilibrium simulation methods can be used to estimate the solubility of amorphous solids. As an illustration, we compute the…
Jarzynski's equality (JE) allows us to compute free energy differences from distributions of work. In molecular dynamics simulations, the traditional way of constructing work distributions is to perform as many pulling simulations as…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…