Related papers: Flexible framework of computing binding free energ…
Free energy calculations in molecular simulations have a variety of applications including determining the strength of molecular processes such as solvation and binding. It has been recently shown that when removing the VDW and Coulomb…
In this review we focus on the determination of phase diagrams by computer simulation with particular attention to the fluid-solid and solid-solid equilibria. The calculation of the free energy of solid phases using the Einstein crystal and…
In this thesis a new model for calculating the total energy of atomic and solid systems is presented. The model is used to study the properties of the Si(100) surface and dislocation dynamics in the diamond structure. For the Si(100)…
We consider the recently developed weighted ensemble milestoning (WEM) scheme [J. Chem. Phys. 152, 234114 (2020)], and test its capability of simulating ligand-receptor dissociation dynamics. We performed WEM simulations on the following…
One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling…
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…
We introduce a simulation technique to compute the free energy difference between two hydrate structures of different stoichiometry connected to a reservoir of gas molecules at a prescribed pressure. The method permits the determination of…
Nuclear binding energies and two-neutron separation energies are analyzed starting from the liquid-drop model and the nuclear shell model in order to describe the global trends of the above observables. We subsequently concentrate on the…
We study the free energy of a heavy quark-antiquark pair in a thermal medium using the AdS/CFT correspondence. We point out that a commonly used prescription for calculating this quantity leads to a temperature dependence in conflict with…
Methods for correcting residual energy errors of configuration interaction (CI) calculations of molecules and other electronic systems are discussed based on the assumption that the energy defect can be mapped onto atomic regions. The…
We propose and justify a new approach for fast calculation of the electrostatic interaction energy of clusters of charged particles in constrained energy minimization in the framework of rigid protein-ligand docking. Our ``blind search''…
The effect of solvent on the free energy of reaction intermediates adsorbed on electrocatalyst surfaces can significantly change the thermochemical overpotential, but accurate calculations of this are challenging. Here, we present…
The Helmholtz free-energy W is calculated as a function of separation distance for two molecules in a fluid, A and B, whose mutual interaction is described by a spherically symmetric potential. For the equilibrium A + B = AB occurring in a…
It can be fruitful to view two-component physical systems of attractive monomers, A and B, ``chemically'' in terms of a reaction A + B <-> C, where C = AB is an associated pair or complex. We show how to construct free energies in the…
Most methods for estimating configurational entropy from molecular simulation data yield upper limits except for harmonic systems where they are exact. Problems arise at diffusive systems and the presence of conformational transitions.…
In the present work, we present a hybrid quantum-classical workflow aimed at improving the accuracy of alchemical free energy (AFE) predictions by incorporating configuration interaction (CI) simulations using the book-ending correction…
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 high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining the excess free energy of the solute. We introduce…
We propose a new method to compute the free energy or enthalpy of fluids or disordered solids by computer simulation . The main idea is to construct a reference system by freezing one representative configuration, and then carry out a…
We present a theoretical first-principles method to calculate the free energy of a magnetic system in its high-temperature paramagnetic phase, including vibrational, electronic, and magnetic contributions. The method for calculating free…