Dynamic
1 - Place all Gaussian outputs (*.out or *.log) in the same
directory.
2 - Open the terminal and navigate to the directory.
3 - Run the command (write only what is after the "$" symbol):
$ run_dyn
4 - Wait until the calculation ends.
Aligment
1 - Put all the folders created by the dynamic in the same
directory.
2 - Create a text file with all the directory names of the dynamic
outputs. Each name must be in each line of the text file and the
text file must be named "names.txt". For example, there are 3
directories: m01, m02 and m03. The text file will be:
m01
m02
m03
You can put them in any order. The text file can be made
manually or by any other way. One of the possibilities is to use
to open the terminal, navigate o the directory containing dynamic
output directories ans use the command:
$ mknames
A "names.txt" text file will be created with a list of all the
directory names. Open it and check if it only contains the output
names.
3 - Create a text file named index.txt. Each line of this file
must contain the atom indexes from Gaussian that will be aligned,
separeted by "tab". For example, the Gaussian atoms indexes of m01
and m02 that will be aligned are 1,3,5,7. For m03 these atoms have
different Gaussian indexes, that are 2,4,5,9. The "names.txt" and
"index.txt" files will be:
"names.txt": "index.txt":
m01 1 3 5 7
m02 1 3 5 7
m03 2 4 5 9
If the "names.txt" file has a different order, the same order must
beused in "index.txt" file:
"names.txt": "index.txt":
m02 1 3 5 7
m03 2 4 5 9
m01 1 3 5 7
4 - Create a new directory in the same one (use only letters and
numbers). Copy both "names.txt" and "index.txt" to the new
directory.
5 - Open the terminal and navigate to that new directory
containing only the files "names.txt" and "index.txt".
6 - Use the command:
$ mk_ndx
A list of index files (*.ndx) will be made.
7 - Choose a molecule to be your alignment reference and rename
its index file adding "_ref" right before the ".ndx". For example,
if the m01 is your reference, the index files must bem named as:
m01_red.ndx
m02.ndx
m03.ndx
8 - Use the command:
$ mk_grid_inps
If there are no index files if the "_ref" afix of if there are
more than one, it will say so. Fix the names and try again. If
it's all correct, the alignment will be made. One directory for
each molecule will be greated plus one named "grid_inps", that
will be used next.
Calculating the descriptors
1 - Open the "grid_inps" directory. Open the text file "box.txt".
It contains the lowest and hights atom locations in each axis in
nanometers. Is indicated to choose box limits igual to +-0.15
nanometer plus the value showed in "box.txt". Than multiply by 10
(to obtain the value in Angstron) and round it to an integer
number. So:
- If it is a minimum number, substract 0.15, multiply by 10 and
round it.
- If it is a maximum number, add 0.15, multiply by 10 and round
it.
For example, for the m01, m02 and m03 the "box.txt" file is:
Coord X Y Z
Min 1.744 1.643 0.446
Max 2.912 2.858 1.594
So the indicated box limits are:
X: -min: round[(1.744 - 0.15)x10] = round[(1.594)x10] =
round[15.94] = 16
-max: round[(2.912 + 0.15)x10] = round[(3.062)x10] =
round[30.62] = 31
Y: -min: round[(1.643 - 0.15)x10] = round[(1.493)x10] =
round[14.93] = 15
-max: round[(2.858 + 0.15)x10] = round[(3.008)x10] =
round[30.08] = 30
Z: -min: round[(0.446 - 0.15)x10] = round[(0.296)x10] =
round[2.96] = 3
-max: round[(1.594 + 0.15)x10] = round[(1.744)x10] =
round[17.44] = 17
2 - The LQTAgridpy program asks for the initial coordinato of the
box and its dimentions.
- The initial coordinates are the minimun box limits. In the
example: 16, 15 and 3, for x, y and z, repectively.
- The box dimentions can be calculated by <max> - <min>. In the
example:
X: (31 - 16) = 15
Y: (30 - 15) = 15
Z: (17 - 3) = 14
3 - The NH3+ is a good probe to use.
4 - The step is 1 angstron usually.
5 - To see the --help of the program, use the command:
$ lqtagridpy -h
6 - The "grid_inps" directory contains a text file named
"list.txt". This is the LQTAgridpy input.
7 - To run the program using this input, the values in the
examples, step 1 and probe NH3+: open the terminal and navigate
too the "grid_inps" directory. Run the command:
$ lqtagridpy --mols list.txt -c 16 15 3 -d 15 15 14 -a NH3+ -s
1 -o matrix.txt
You can change the output name by changing the "matrix.txt"
part.
Your output will be generated.
