Robust Free Energy Perturbation Protocols for Creating Molecules in Solution.

ABSTRACT: Accurate methods to estimate free energies play an important role for studying diverse condensed-phase problems in chemistry and biochemistry. The most common methods used in conjunction with molecular dynamics (MD) and Monte Carlo statistical mechanics (MC) simulations are free energy perturbation (FEP) and thermodynamic integration (TI). For common applications featuring the conversion of one molecule to another, simulations are run in stages or multiple "λ-windows" to promote convergence of the results. For computation of absolute free energies of solvation or binding, calculations are needed in which the solute is typically annihilated in the solvent and in the complex. The present work addresses identification of optimal protocols for such calculations, specifically, the creation/anni

SUBMITTER: Cabeza de Vaca I 

PROVIDER: S-EPMC6615964 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature