Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics

Finite temperature free energy calculations in NWChem: Metadynamics and Umbrella Sampling-WHAM

Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model

Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower lev...

Metadynamics with Adaptive Gaussians.

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 Gaussian potentials of preassigned and typically diagonal covariance. Asymptotically the free-energy surface is proportional to the bias deposited. Here, we co...

Calculating Thermodynamics Properties of Classical and Quantum Systems by a Metadynamics Monte Carlo Procedure

This thesis presents a new metadynamics-based quantum Monte Carlo approach to compute the phase diagram and equilibrium properties of condensed matter systems typically quantum solids whose Hamiltonian contain important and dominant quantum effects. Two main applications are presented the classical and the quantum Ising model. Using path integral Monte Carlo we study the re-entrant phase diagra...

Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics

The protein mediated hydrolysis of nucleoside triphosphates such as ATP or GTP is one of the most important and challenging biochemical reactions in nature. The chemical environment (water structure, catalytic metal, and amino acid residues) adjacent to the hydrolysis site contains hundreds of atoms, usually greatly limiting the amount of the free energy sampling that one can achieve from compu...