Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
|Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
|Year of Publication
|Morreale, Antonio, de la Cruz Xavier, Meyer Tim, Gelpí Josep-Lluis, F Luque Javier, and Orozco Modesto
|2004 Nov 15
|Alanine, Algorithms, Chemical, Computer Simulation, Databases, Humans, Models, Peptides, Poisson Distribution, Protein, Proteins, Solvents, Static Electricity, Thermodynamics, Time Factors, Water
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.