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

Proteins
Antonio MorrealeM Orozco

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.

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Citations

May 11, 2006·Chemical Reviews·Ninad Prabhu, Kim Sharp
Sep 27, 2006·Protein Science : a Publication of the Protein Society·David TalaveraModesto Orozco
Dec 20, 2016·The Journal of Physical Chemistry. B·Shu-Ching OuB Montgomery Pettitt
Feb 11, 2010·Physical Chemistry Chemical Physics : PCCP·Agnes NoyModesto Orozco
Nov 8, 2007·Journal of the American Chemical Society·Alberto PérezModesto Orozco
Sep 1, 2005·Journal of Chemical Theory and Computation·Alberto PérezModesto Orozco

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