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Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?

Posted June 8th, 2010 by pschmidtke
TitleLinear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
Publication TypeJournal Article
Year of Publication2004
AuthorsMorreale, A, de la Cruz X, Meyer T, Gelpi JL, Luque FJ, Orozco M
JournalProteins
Volume57
Issue3
Pagination458 - 467
Date Published2004/11/15/
KeywordsAlanine/chemistry; Algorithms; Computer Simulation; Databases, Chemical; Peptides/chemistry; Poisson Distribution; Proteins/chemistry; Solvents/chemistry; Static Electricity; Thermodynamics; Time Factors; Water/chemistry, Protein; Humans; Models
AbstractWe 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.