Escaping free-energy minima
Reads0
Chats0
TLDR
A powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates is introduced.Abstract:
We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.read more
Citations
More filters
Journal ArticleDOI
Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems
TL;DR: Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids).
Journal ArticleDOI
Unsupervised machine learning in atomistic simulations, between predictions and understanding
TL;DR: In this paper, the authors discuss the importance of using concise yet complete representations of atomic structures as the starting point of the analyses, and highlight the risk of introducing preconceived biases when using machine learning to rationalize and understand structure-property relations.
Journal ArticleDOI
Characterizing Drug–Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches
TL;DR: This work proposes to use the optimized (or minimized) structures derived from holo-state proteins to calculate drug residence time, which could give a comparable or even better prediction accuracy compared with those calculated utilizing a large number of molecular dynamics structures based on the Poisson process.
Journal ArticleDOI
Combining Evolutionary Algorithms with Clustering toward Rational Global Structure Optimization at the Atomic Scale.
TL;DR: This work combines an evolutionary algorithm (EA) and clustering, a machine-learning technique, to produce a rational algorithm for global structure optimization that proves significantly faster when favoring stable structures in unexplored regions.
Journal ArticleDOI
Measuring liquid crystal elastic constants with free energy perturbations
Abhijeet A. Joshi,Jonathan K. Whitmer,Jonathan K. Whitmer,Orlando Guzmán,Nicholas L. Abbott,Juan J. de Pablo,Juan J. de Pablo +6 more
TL;DR: A first principles method is proposed to calculate the Frank elastic constants of nematic liquid crystals including the constants corresponding to standard splay, twist and bend deformations, and an often-ignored surface-like contribution known as saddle-splay which is found to exist at the limits of the Ericksen inequalities governing positive definite free energy.
References
More filters
Journal ArticleDOI
Optimization by Simulated Annealing
TL;DR: There is a deep and useful connection between statistical mechanics and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters), and a detailed analogy with annealing in solids provides a framework for optimization of very large and complex systems.
Journal ArticleDOI
Efficient, multiple-range random walk algorithm to calculate the density of states.
Fugao Wang,David P. Landau +1 more
TL;DR: A new Monte Carlo algorithm is presented that permits us to directly access the free energy and entropy, is independent of temperature, and is efficient for the study of both 1st order and 2nd order phase transitions.
Journal ArticleDOI
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
TL;DR: In this article, a general method for accelerating the molecular-dynamics (MD) simulation of infrequent events in solids is derived, and the diffusion mechanism of a 10-atom Ag cluster on the Ag(111) surface using a $220\ensuremath{\mu}\mathrm{s}$ hyper-MD simulation.
Journal ArticleDOI
Constrained reaction coordinate dynamics for the simulation of rare events
TL;DR: In this article, a computationally efficient molecular dynamics method for estimating the rates of rare events that occur by activated processes is described, where the system is constrained at bottleneck regions on a general many-body reaction coordinate in order to generate a biased configurational distribution.
Journal ArticleDOI
Free energy from constrained molecular dynamics
Michiel Sprik,Giovanni Ciccotti +1 more
TL;DR: In this article, the blue-moon ensemble method was used to compute the potential of mean force and transmission coefficient of a given reaction coordinate in the case of an arbitrary reaction coordinate.