Paper Citing NAMD - Abstract
Singharoy, Abhishek; Joshi, Harshad; Miao, Yinglong; Ortoleva, Peter J.
Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Macromolecular Assemblies
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8423-8434, JUL 26 2012
Coarse-grained features of macromolecular assemblies are understood via a set of order parameters (OPs) constructed in terms of their all atom configuration. OPs are shown to be slowly changing in time and capture the large-scale spatial features of macromolecular assemblies. The relationship of these variables to the classic potion of OPs based on symmetry breaking phase transitions is discussed. OPs based on space warping transformations are analyzed in detail as they naturally provide a connection between overall structure of an assembly and all-atom configuration. These OPs serve as the basis of a multiscale analysis that yields Langevin equations for OP dynamics. In this context, the characteristics of OPs and PCA modes are compared. The OPs enable efficient all atom multiscale simulations of the dynamics of macromolecular assemblies in response to changes in microenvironmental conditions, as demonstrated on the structural transitions of cowpea chlorotic mottle virus capsicl (CCMV) and RNA of the satellite tobacco mosaic virus (STMV).
