Quantifying Solvation Effects on Peptide Conformations: A QM/MM Replica Exchange Study

Abstract

We present replica exchange molecular dynamics calculations of the conformational space of alanine dipeptide, both in the gas phase and in water using both a classical force field potential and several commonly used semi-empirical QM/MM Hamiltonians implemented within the latest version of the AMBER software suite. We present results comparing the performance of each method with experimental data for Ramachandran conformational distributions, NMR J coupling estimates and radial distribution functions for the peptide–solvent interactions.