Related papers: Predicting binding free energies in solution
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…
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…
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…
The uniform electron gas is a key model system in the description of matter, including dense plasmas and solid state systems. However, the simultaneous occurence of quantum, correlation, and thermal effects makes the theoretical description…
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of "bridging" potential energy…
The hydration or binding free energy of a drug-like molecule is a key data for early stage drug discovery. Hundreds of thousands of evaluations are needed, which rules out the exhaustive use of atomistic simulations and free energy methods.…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
The solvation free energy (SFE) of molecules and ions is a fundamental property governing their solvation behavior and solubility. Molecular simulations offer a route to compute SFEs using alchemical free energy methods, such as…
Simple analytic formulae for energy relaxation (ER) in electron-ion systems, with quantum corrections, ion dynamics and RPA-type screening are presented. ER in the presence of bound electrons is examined in view of of recent simulations for…
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…
We study alchemical atomic energy partitioning as a method to estimate atomisation energies from atomic contributions which are defined in physically rigorous and general ways through use of the uniform electron gas as a joint reference. We…
Sequences of experimental ground-state energies are mapped onto concave patterns cured from convexities due to pairing and/or shell effects. The same patterns, completed by a list of excitation energies, can be used to give numerical…
Classical density-functional theory is the most direct approach to equilibrium structures and free energies of inhomogeneous liquids, but requires the construction of an approximate free-energy functional for each liquid of interest. We…
The expression of the free energy of a liquid in terms of an explicit decomposition of the particle configurations into local coordination clusters is examined. We argue that the major contribution to the entropy associated with structural…
In aqueous solutions, dissolved ions interact strongly with the surrounding water, thereby modifying the solution properties in an ion-specific manner. These ion-hydration interactions can be accounted for theoretically on a mean-field…
Neutral molecules with sufficiently large dipole moments can bind electrons in diffuse nonvalence orbitals with most of their charge density far from the nuclei, forming so-called dipole-bound anions. Because long-range correlation effects…
Accurately simulating the properties of liquid water remains a central challenge in molecular simulations. In this work, we use machine learning potentials to investigate how the convergence settings of electronic structure calculations…
Quantitative evaluations of the free energy of materials must take into account thermal and zero-point energy fluctuations. While these effects can easily be estimated within a harmonic approximation, corrections arising from the anharmonic…
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, due to the availability of only a finite number of data values, N. Free energy differences (DF) between two states or systems are critically important…
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…