Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
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.
Morreale
Antonio
A
Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Barcelona, Spain.
de la Cruz
Xavier
X
Meyer
Tim
T
Gelpí
Josep Lluís
JL
Luque
F Javier
FJ
Orozco
Modesto
M
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*
D010455:Peptides; D011506:Proteins; D012997:Solvents; D014867:Water; D000409:Alanine