title: Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
abstract: We explore the use of classical Linear Response Theory (LRT) as an alternative strategy to the use of Molecular Mechanics/Poisson-Boltzmann strategies to compute the solvation free energy of macromolecules from molecular dynamics simulations using an explicit representation of solvent. The method reproduces well the free energy of solvation of standard amino acid side chains, small peptides, and proteins. The use of a fully discrete representation of solvent avoids the possible problems of continuum models to represent the solvation of systems containing tightly bound water molecules.
authors.affiliation: Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Barcelona, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Morreale
authors.forename: Xavier
authors.initials: X
authors.lastname: de la Cruz
authors.forename: Tim
authors.initials: T
authors.lastname: Meyer
authors.forename: Josep Lluís
authors.initials: JL
authors.lastname: Gelpí
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Luque
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
mesh_terms: D000409:Alanine / Q000737:chemistry; D000465:Algorithms; D003198:Computer Simulation; D030562:Databases, Protein; D006801:Humans; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry; D016012:Poisson Distribution; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry*
chemical_list: D010455:Peptides; D011506:Proteins; D012997:Solvents; D014867:Water; D000409:Alanine