Paper Citing NAMD - Abstract
Menor, S. A.; de Graff, Adam M. R.; Thorpe, M. F.
Hierarchical plasticity from pair distance fluctuations
PHYSICAL BIOLOGY, 6 Art. No. 036017, SEP 2009
Observations, experiments and simulations often generate large numbers of snapshots of configurations of complex many-body systems. It is important to find methods of extracting useful information from these ensembles of snapshots in order to document the motion as the system evolves in time. Some of the most interesting information is contained in the relative motion of individual constituents, rather than their absolute motion. We present a novel statistical method for identifying hierarchies of plastically connected objects in a system from a series of two or more snapshot configurations. These plastic clusters are distinctive in that although their members tend to remain loosely connected, the clusters may be deformed plastically. This method is demonstrated for a number of systems, including an exactly soluble freely jointed polymer chain model, a two-dimensional simulation of two species of interacting bodies and a protein. These concepts are implemented as TIMME, the Tool for Identifying Mobility in Macromolecular Ensembles.
