Mod:Hunt Research Group/UseNCIPlot

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:"

-----------------------------------------------------
      Operating grid and increments:
-----------------------------------------------------
 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

generating the traditional rho vs rdg

• rdg=reduced density gradient
• this is in the *.dat file

there are a huge number of points, not ordered, plotting is really slow!

• use the python script nci_plot.py to make managable and ready to plot

nci_plot.py file_name (without .dat extension)

this will reduce the limits for the rdg (x-axis)

first two columns are rho and full rdg then

4 columns for plotting the data, low (blue), middle (green) and high(red) values

because the "nonvalues" are set to 0.0 there is also a column of zero's which you make white to hide the other column entries in the graph

remember rdg is on the x-axis!

you can run nci_plot.py with the defaults or set the rdg limits and colour change value cut-off

default is limit =0.06 and colour change at cut-off=±0.02

nci_plot.py file_name cut-off (for colours) limit (rdg)

• find nci_plot.py here nci plot code

using VMD to visualise

• the VMD script works well

in VMD cd into the directory with your files

select load state and then the filename.vmd

• make it look better

I like to have more light and to turn off depth queuing

so add the following to the file

axes location off
display depthcue off
# change the background colour
color display background iceblue
# change the color individual elements 
color element P orange2
# there is a bug and this command won’t work you have to do it manually: colour element C grey

• then render with tachyon

render Tachyon image1 "/Applications/tachyon/compile/macosx-x86-thr/tachyon" -aasamples 12 %s -fullshade -auto_skylight 0.5 -res 600 600  -format TARGA -o %s.tga

OR

render Tachyon image1 "/Applications/tachyon/compile/macosx-x86-thr/tachyon" -aasamples 12 %s -fullshade -res 600 600  -format TARGA -o %s.tga