Related papers: Adaptively Biased Molecular Dynamics for Free Ener…
Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling…
We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is…
Metadynamics is an established sampling method aimed at reconstructing the free-energy surface relative to a set of appropriately chosen collective variables. In standard metadynamics the free-energy surface is filled by the addition of…
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when multiple parallel channels along the reaction coordinate or hidden barriers in directions…
We introduce an efficient and robust method to compute alchemical free energy differences, resulting from the application of multiple walker Adaptive Biasing Force (ABF) in conjunction with strongly damped Langevin $\lambda$-dynamics.…
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled…
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated…
Enhanced sampling and free energy calculation algorithms of the Thermodynamic Integration family (such as the Adaptive Biasing Force method, ABF) are not based on the direct computation of a free energy surface, but rather of its gradient.…
We propose a formulation of adaptive computation of free energy differences, in the ABF or nonequilibrium metadynamics spirit, using conditional distributions of samples of configurations which evolve in time. This allows to present a truly…
Conventional molecular dynamics (MD) simulation approaches, such as $\textit{ab initio}$ MD (AIMD) and empirical force field MD (EFFMD), face significant trade-offs between physical accuracy and computational efficiency. This work presents…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
A thin plate or slab, prepared so that opposite faces have different surface stresses, will bend as a result of the stress difference. We have developed a classical molecular dynamics (MD) formulation where (similar in spirit to…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
We present convergence results for an adaptive algorithm to compute free energies, namely the adaptive biasing force (ABF) method. The free energy is the effective potential associated to a so-called reaction coordinate (RC). Computing free…
Biased sampling in molecular dynamics simulations overcomes timescale limitations and delivers free-energy landscapes, essential to understand complex atomistic phenomena. However, when applied across diverse systems and processes, biasing…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…