Paper Citing NAMD - Abstract
Shah, Manas; Santiso, Erik E.; Trout, Bernhardt L.
Computer Simulations of Homogeneous Nucleation of Benzene from the Melt
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10400-10412, SEP 8 2011
Nucleation is the key step in crystallization by which the molecules (or atoms or ions) aggregate together, find the right relative orientations, and start to grow to form the final crystal structure. Since nucleation is an activated step involving a large gap in time scales between molecular motions and the nucleation event itself, nucleation must be studied using rare events methods. We employ a technique developed previously in our group known as aimless shooting [Peters, B.; Trout, B. L. J. Chem. Phys., 2006, 125, 054108], which is based on transition path sampling, to generate reactive trajectories between the disordered and ordered phases of benzene. Using the likelihood maximization algorithm, we analyze the aimless shooting trajectories to identify the key order parameters or collective variables to describe the reaction coordinate for the nucleation of benzene from the melt. We find that the local bond orientation and local relative orientation order parameters are the most important collective variables in describing the reaction coordinate for homogeneous nucleation from the melt, as compared to cluster size and space-averaged order parameters. This study also demonstrates the utility of recently developed order parameters for molecular crystals [Santiso, E. E.; Trout, B. L. J. Chem. Phys., 2011, 134, 064109].
