Related papers: Best Practices for Alchemical Free Energy Calculat…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
Free energy calculations are widely used tools in computational chemistry, but their dependence on the assignment of partial charges during force field parametrization reduces their accuracy and reproducibility. In this work, we highlight…
The proposed method of the free energy calculation is based on the approximation of the energy distribution in the microcanonical ensemble by the Gaussian distribution. We hope that our approach will be effective for the systems with…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
Absolute Binding Free Energy (ABFE) methods are among the most accurate computational techniques for predicting protein-ligand binding affinities, but their utility is limited by the need for many simulations of alchemically modified…
This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration. We employ linear regression to construct a polynomial that optimally fits the thermodynamic integration…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…
Alchemical Grid Dock (AlGDock) is open-source software designed to compute the binding potential of mean force (BPMF) - the binding free energy between a flexible ligand and a rigid receptor - for a small organic ligand and a biological…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
The computational treatment of many-electron systems capable of exchanging {electrons and nuclei} with the environment represents one of the outermost frontiers in simulation methodology. The exchanging process occurs in a large variety of…
To calculate the temperature at which a first-order cosmological phase transition occurs, one must calculate $F_c(T)$, the free energy of a critical bubble configuration. $F_c(T)$ is often approximated by the classical energy plus an…
Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I…
We apply energy landscape methods to digital alchemy, defining a system in which the parameters of the potential are treated as degrees of freedom. Using geometrical optimisation, we locate minima and transition states on the landscape for…
While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular…
An overview of quantum-mechanical methods to generate cross-section data for electron collisions with atoms and molecules is presented. Particular emphasis is placed on the time-independent close-coupling approach, since it is particularly…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from…
A controllable energy method, which considers the undersampling issue of the transfer function and valid spectral energy of a source signal, is proposed to implement angular spectrum diffraction calculation in near and far fields. The…
Free energy and entropy are examined in detail from the standpoint of classical thermodynamics. The approach is logically based on the fact that thermodynamic work is mediated by thermal energy through the tendency for nonthermal energy to…