Paper Citing NAMD - Abstract
Duff, Nathan; Peters, Baron
Polymorph specific RMSD local order parameters for molecular crystals and nuclei: alpha-, beta-, and gamma-glycine
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 134101, OCT 7 2011
Crystal nucleation is important for many processes including pharmaceutical crystallization, biomineralization, and material synthesis. The progression of structural changes which occur during crystal nucleation are often described using order parameters. Polymorph specific order parameters have been developed for crystallization of spherically symmetric particles; however, polymorph specific order parameters for molecular crystals remain a challenge. We introduce template based polymorph specific order parameters for molecular crystals. For each molecule in a simulation, we compute the root mean squared deviation (RMSD) between the local environment around the molecule and a template of the perfect crystal structure for each polymorph. The RMSD order parameters can clearly distinguish the alpha-, beta-, and gamma-glycine polymorph crystal structures in the bulk crystal and also in solvated crystallites. Surface melting of glycine crystallites in supersaturated aqueous solution is explored using the newly developed order parameters. The solvated alpha-glycine crystallite has a thinner surface melted layer than the gamma-glycine crystallite. alpha-glycine forms first out of aqueous solution, so surface melted layer thickness may provide insight into interfacial energy and polymorph selection. (C) 2011 American Institute of Physics. [doi:10.1063/1.3638268]
