Paper Citing NAMD - Abstract
Baer, M.; Schreiner, E.; Kohlmeyer, A.; Rousseau, R.; Marx, D.
Inverse temperature transition of a biomimetic elastin model: Reactive flux analysis of folding/unfolding and its coupling to solvent dielectric relaxation
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3576-3587, MAR 2 2006
The inverse temperature transition (ITT) of a biomimetic model for elastin, capped GVG(VPGVG) in liquid water, is investigated by a comprehensive classical molecular dynamics study. The temperature dependence of the solvation structure and dynamics of the octapeptide are compared using three common force fields, CHARMM, GROMOS, and OPLS. While these force fields differ in quantitative detail, they all predict this octapeptide to undergo a "folding transition" to closed conformations upon heating and a subsequent "unfolding transition" to open conformations at still higher temperatures, thus reproducing the ITT scenario. The peptide kinetics is analyzed within the reactive flux formalism applied to the largest-amplitude mode extracted from principal component analysis, and the solvent's dielectric fluctuations are obtained from the total water dipole autocorrelations. Most importantly, preliminary evidence for an intimate coupling of peptide folding/unfolding dynamics, and thus the ITT, and dielectric relaxation of bulk water is given, possibly being consistent with a "slave mode" picture.
