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Linear response theory: An alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
Author(s) -
Morreale Antonio,
de la Cruz Xavier,
Meyer Tim,
Gelpí Josep Lluís,
Luque F. Javier,
Orozco Modesto
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20169
Subject(s) - solvation , molecular dynamics , representation (politics) , implicit solvation , statistical physics , computational chemistry , molecular mechanics , poisson–boltzmann equation , molecule , chemistry , chemical physics , physics , organic chemistry , ion , politics , political science , law
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. Proteins 2004. © 2004 Wiley‐Liss, Inc.