Paper Citing NAMD - Abstract
Zhang, Dajun; Chippada, Uday; Jordan, Kenneth
Effect of the structural water on the mechanical properties of collagen-like microfibrils: A molecular dynamics study
ANNALS OF BIOMEDICAL ENGINEERING, 35:1216-1230, JUL 2007
The objective of this paper is to investigate the role played by the structural water on the intermolecular sliding between collagen-like 1QSU peptides in a microfibril under deformation. Three modes of deformation are used to generate intermolecular sliding: forced axial stretching (case I) or sliding (case II) of a central peptide monomer (while other surrounding monomers are fixed); and cantilever bending (case III) under a terminal lateral load. The force-displacement curve of each deformation mode is derived using a module called Steered Molecular Dynamics (SMD) in a molecular dynamics package NAMD under the CHARMM22 force field. Each calculation is carried out twice, one in the presence of structural water, one without. It is found that the structural water is a weak "lubricant" in forced axial stretching (case I), but it functions as a "glue" in forced axial sliding (case II) and cantilever bending (case III). A change in the pulling speed does not significantly alter the force-displacement behavior in axial stretching (case I) and sliding (case II), but it does in cantilever bending (case III). The additional resistance contributed by the structural water is attributed to the additional energy cost in breaking the water-mediated hydrogen bonds (water bridges).
