Molecular dynamics simulations have been performed to compute the solvation free energy
and the octanol/water partition coefficients for a challenging set of selected organic …

Alchemical free energy calculations are an increasingly important modern simulation
technique to calculate free energy changes on binding or solvation. Contemporary …

In the context of drug–receptor binding affinity calculations using molecular dynamics
techniques, we implemented a combination of Hamiltonian replica exchange (HREM) and a …

Rigorous binding free energy methods in drug discovery are growing in popularity because
of a combination of methodological advances, improvements in computer hardware, and …

We developed a novel force field in the context of AMBER parameterization for glutamate
and aspartate zinc (II)-binding residues. The interaction between the zinc ion and the …

We investigate the role of order/disorder transitions in alchemical simulations of protein-
ligand absolute binding free energies. We show, in the context of a potential of mean force …

We present a new release (6.0 β) of the ORAC program [Marsili et al. J. Comput. Chem.
2010, 31, 1106–1116] with a hybrid OpenMP/MPI (open multiprocessing message passing …

In this paper, we compute, by means of a non equilibrium alchemical technique, called fast
switching double annihilation methods (FSDAM), the absolute standard dissociation free …

The recently proposed fast switching double annihilation (FS-DAM)[Cardelli et al., J. Chem.
Theory Comput., 2015, 11, 423] is aimed at computing the absolute standard dissociation …

The partitioning of solute molecules between immiscible solvents with significantly different
polarities is of great importance. The polarization between the solute and solvent molecules …