# new feature: isosurface NCI (noncovalent interactions) # # references: # # "Revealing Noncovalent Interactions", # Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia Contreras-Garcia, Aron J. Cohen, and Weitao Yang, # J. Am. Chem. Soc., 2010, 132, 6498-6506. email to julia.contreras@duke.edu # # "NCIPLOT: A Program for Plotting Noncovalent Interaction Regions" # Julia Contreras-García, Erin R. Johnson, Shahar Keinan, Robin Chaudret, Jean-Philip Piquemal, David N. Beratan, and Weitao Yang, # J. of Chemical Theory and Computation, 2011, 7, 625-632 # # # -- NCIPLOT promolecule calculation for reduced density. # Plots reduced density mapped with ABS(rho)*SIGN(lambda2) # where lambda2 is the middle eigenvalue of the Hessian matrix of # promolecular electron density. Innovates a discrete SCF option not # available in NCIPLOT itself. # # default is "promolecular" approximation # # isosurface NCI # # DISCRETE SCF -- starting with standard CUBEGEN file # # isosurface NCI "density.cube" # # DISCRETE SCF -- starting with NCIPLOT's xx-nci-dens.cube file # # isosurface parameters [0 0 0 0 0 0.01] NCI "dens.cube" # # Isosurface parameters [cutoff, p1, p2, p3, p4] NCI ... # # -- p1 = 0(all, default), 1(intramolecular), 2(intermolecular) # -- p2 = rhoMin (min rho cutoff to remove very low density points) # -- p3 = rhoPlot (cutoff used to remove covalent density, default 0.07 for promolecular, 0.05 for SCF) # -- p4 = rhoParam (fraction of total rho that defines intramolecular, default 0.95) # -- p5 = dataScaling (default 1, but set to 0.01 to read back in NCIPLOT -dens.cube file) # # for example: # # isosurface parameters [0 1] NCI "density.cube" (discrete SCF NCI with intramolecular option) # isosurface parameters [0 2] NCI "density.cube" (discrete SCF NCI with intermolecular option) # isosurface parameters [0 -1] NCI "grad.cube" MAP "dens.cube" (intramolecular filtering of NCIPLOT cubes) # isosurface parameters [0 -2] NCI "grad.cube" MAP "dens.cube" (intermolecular filtering of NCIPLOT cubes) # # # In addition, NCI promolecular calculations can be carried out also using # # contact {...} {...} NCI #