Related papers: Single-Sweep Methods for Free Energy Calculations
A mixed basis approach based on density functional theory is employed for low dimensional systems. The basis functions are taken to be plane waves for the periodic direction multiplied by B-spline polynomials in the non-periodic direction.…
Ab initio metadynamics enables extracting free-energy landscapes having the accuracy of first principles electronic structure methods. We introduce an interface between the PLUMED code that computes free-energy landscapes and…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and…
Sampling the free energy surface, namely, the distribution of collective variables (CVs), is a crucial problem in statistical physics, as it underpins a better understanding of chemical reactions and conformational transitions. Traditional…
We propose finite-volume schemes for the Cahn-Hilliard equation which unconditionally and discretely preserve the boundedness of the phase field and the dissipation of the free energy. Our numerical framework is applicable to a variety of…
Free energy calculations of two crystalline phases of the molecular compound S8 were performed via molecular dynamics simulations of these crystals. The elemental sulphur S8 molecule model used in our MD calculations consists of a…
The multistate Bennett acceptance ratio (MBAR) method is a prevalent approach for computing free energies of thermodynamic states. In this work, we introduce BayesMBAR, a Bayesian generalization of the MBAR method. By integrating…
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that…
The accurate treatment of long-range energy terms such as van der Waals interactions is crucial for reliable free energy calculations in molecular simulations. Methods like force switching, potential switching, potential shifting, and Ewald…
A key challenge for molecular dynamics simulations is efficient exploration of free energy landscapes over relevant collective variables (CV). Common methods for enhancing sampling become prohibitively inefficient beyond only a few CVs; in…
We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from…
We introduce a novel scheme for the mechanistic investigation of solid-solid phase transitions, which we dub \textit{metashooting}. Combining transition path sampling molecular dynamics and metadynamics, this scheme allows for both a…
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…
Free energy sampling methods allow studying the full dynamics of activated processes. Unfortunately, the affordable accuracy of the potential describing the energy and forces of the system is usually rather low. Here we introduce a new…
A `polydisperse' system has an infinite number of conserved densities. We give a rational procedure for projecting its infinite-dimensional free energy surface onto a subspace comprising a finite number of linear combinations of densities…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling [Skilling J. (2004) In AIP Conference Proceedings, vol. 735, p. 395.; Skilling…
Dynamical energy analysis was recently introduced as a new method for determining the distribution of mechanical and acoustic wave energy in complex built up structures. The technique interpolates between standard statistical energy…
We present a new method, in the following called MMM2D, to accurately calculate the electrostatic energy and forces on charges being distributed in a two dimensional periodic array of finite thickness. It is not based on an Ewald summation…