Using NCI Plot
basics
- first you need to generate a *.wfn file, run Gaussian and use the keyword OUTPUT=WFN in the command line and add a single extra line identifying the *.wfn file
- create an input file called "input.nci" the basic that you need are 3 lines, the first line is 1 (number of files to be analysed), the second line gives the name of the *.wfn file, on the third line is a command for the maximum level of output "OUTPUT 3", for example see the "nciplot.input" file below
1
BARF2Cl_HSiEt3_m062x_6311g_wfn.wfn
OUTPUT 3
- run the program by typing nciplot input.nci
- to send the standard output to a file type nciplot input.nci file.out
- once completed to view the surface start up VMD and under "file" choose "load visualisation state"
- blue for H-bonding, covalent
- green for van der Waals (attractive)
- red for steric (repulsive)
options
- specifying output 3 produces a range of files
- name.dat is rho vs s(r)
- name-grad.cube is the cube file containing s(r)
- name-dens.cube is the cube file containing sign(lambda2)*rho*100
- name.vmd is a script for visualization of the results in VMD
- the s(r) range default can be a bit wide if you are looking only at non-covalent interactions, try
- cutoffs 0.1 2.0
- the first is for s(r) (y-axis) and the second is for rho (x-axis) (this is contrary to the manual!)
- also in the data file, the first column (x axis) is sign(lambda2)*rho*100 and the second is s(r)
- the density is analysed on a cube file
- the manual indicated the cube is evaluaated on the molecular coordinates with +/- 2au added to each direction
- you might need to alter these
- if you get some excess bits appearing you might need to reduce the area covered
- display the axes at the origin, then work out where the excess is
- look in the output file for "Operating grid and increments:"
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Operating grid and increments:
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x0,y0,z0 = -12.9607 -10.6552 -7.1674
x1,y1,z1 = 10.8589 12.2604 11.3459
ix,iy,iz = 0.10 0.10 0.10
nx,ny,nz = 239 230 186
- x0 etc give the starting points and x1 etc give the ending points
- to change the range fix this via a command in the input file specifying smaller limits
- key command is CUBE x0 y0 z0 x1 y1 z1
