Genetic Algorithm search for collective variables
(c) Antti-Pekka Hynninen, 2014
[email protected]

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Compiling:
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make

Use "make clean" to clean up the build

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Running: cv input_file.inp
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cv input_file.inp

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Example:
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See example -directory for an example run.
You can run the example by going in to the "example" -directory and typing
../cv cv.inp

The input file in the example is the following:

--------- cv.inp -----------
num_cv 2                     # number of collective variables
num_shoot 20000              # number of shooting points
num_coord 73                 # number of coordinates per shooting point
num_gene 500                 # number of genes in the population (e.g. population size)
num_iter 100                 # number of iterations to perform in the GA
filename_coord coords.txt    # filename for shooting point coordinates
filename_hAB 20k_hAB.txt     # filename for shooting end points
p_mutate 0.1                 # mutation rate for the GA
----------------------------

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File formats:
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The shooting point coordinate file lists coordinates for every shooting point
after another:

Lines 1             to   num_coord are shooting point 1 coordinates
Lines num_coord+1   to 2*num_coord are shooting point 2 coordinates
Lines 2*num_coord+1 to 3*num_coord are shooting point 3 coordinates
...
Lines (num_shoot-1)*num_coord+1 to num_shoot*num_coord are shooting point
num_shoot coordinates

In total then the file has num_shoot*num_coord lines. Each line has the
atom info in the PDB file format:

ATOM   2976  N   GLU   212      -1.000   0.454   9.001  0.00  0.00
ATOM   2977  HN  GLU   212      -1.539  -0.142   9.592  0.00  0.00
ATOM   2978  CA  GLU   212      -1.339   0.630   7.631  0.00  0.00
ATOM   2979  HA  GLU   212      -0.934   1.530   7.192  0.00  0.00
....

This format can be build from multiple .pdb files using the "cut.sh" script,
see next section.

Shooting end point file format is:

    1 1 0 1 0
    2 1 0 1 0
    3 1 0 1 0
    4 0 1 1 0
    ...

19998 1 0 1 0
19999 1 0 1 0
20000 1 0 1 0

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cut.sh script
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cut_coord/cut.sh        - script
cut_coord/residues.txt  - residue selection

cut.sh script can be used to cut out select residues from multiple .pdb files.
Note that the residue names mush exactly match, including whitespace, the
residue names in the .pdb files. This is because the script uses a grep.