Steered molecular dynamics (SMD) has been seen to provide the potential of mean force (PMF) along a peptides unfolding reaction coordinate, but SMD comes at a significant computational cost. The characterization of the conformation changes and energetcis of the unfolding pathway of proteins offers insight into the relationship between the reaction pathway and the corresponding structure relative to the PMF. Our method, adaptive steered molecular dynamics (ASMD), has previously been shown for the a � helical peptide decaalanine, to be both accurate and computational efficienct for relating the conformational changes and energetics through the PMF. In this work, ASMD is used in conjunction with the CHARMM and AMBER force fields at several different pulling velocities and in three different environments: vacuum, and the implicit and explicit water solvent models. Through the analysis of the PMF and the hydrogen bonding structures over the course of the peptides mechanical unfolding pathway, the differences in the force fields can be analyzed.

Direct comparison of the energetics of decaalanine in the CHARMM and AMBER force fields

248th National Meeting (2014)

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