This is release 1.0 of Axial Frequency Distribution (AFD). 

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*********INPUT FILE**************
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The content of input file will be

trajin test.mdcrd
afd test-coordinate.out 0.1 5 :198@O :374@H18

"trajin" can be given multiple times, but it is preferable if you merge your trajectory into a single file with periodic boundary condition. 

"afd" must have a single instance and the order of the arguements should be preserved. 
First arguement is the output filename, second is the bin size, third is the length of axis to be accessed in Angstrom, forth and fifth arguement are the entities for the bi-molecular interaction.
Atom mask is similar to the mask of amber. :198 is the residue number 198 and @O is the carbonyl oxygen atom of the backbone of residue 198. Similar the second mask represent the atom H18 of residue 374. Residue number should be used instead of residue name.
The matrix will be centered on forth arguement and distribution of the fifth will be written according to its relative coordinates in the trajectory file.

The matrix generated will be of the size (axis-length/bin-size)*2 and in this case it will be (5/0.1)* 2 = 100. So, the matrix size will be of 100 X 100.

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*********RUNINNG AFD*************
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Execution command:

The AFD can be executed using the following command

<program> -i <input-parameter-file> -p <topology-file>

Example

AFD -i test.in -p test.prmtop

Sample files can be downloaded from 
http://ncb.qau.edu.pk/index.php/people/faculty/16-dr-syed-sikander-azam.html
http://ncb.qau.edu.pk/drsikander/

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******DISPLAYING RESULTS*********
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Following script of MatLab should run to visualize a matrix of 100 X 100 generated from a bin size of 0.1 and axis length of 5 by AFD

[Z]= reshape(textread('test-coordinate.out','%n'),100,100)
[X,Y]=meshgrid(-5:.1:5)
Z(Z==0)=NaN
mesh(Z)

This will give you a graph as an output depicting the axial distribution for the required entities within different time span of simulation exhibiting their dynamical pattern on relative time scale. The MatLab graph will show a gradient picture of a density distribution of molecular entities on the XY plane.  The Z plane represents the density distribution while overall graph gives rise to interpret various interactions and rotations which can be significant especially in biological and chemical phenomena.