Parameter distribution during simulation

This can be used to calculate distribution of a parameter of either a specific base-pair/step or over a DNA segment during the simulations.


usage: dnaMD histogram [-h] [-i L-BP_cdna.dat] [-o output.dat]
                       [-tbp total-bp-number] [-bins bins] [-p parameter]
                       [-bs bp/s-start-number] [-be bp/s-end-number]
                       [-mm sum-or-mean] [-fbp 1]

Optional arguments:

-h, --help            show this help message and exit
-i L-BP_cdna.dat, --input L-BP_cdna.dat
                    Name of input file (from do_x3dna or hdf5 file).
                    This file should contain the required parameters. It can be a file either
                    produced from do_x3dna or hdf5 storage file.

-o output.dat, --output output.dat
                    Name of output file.
                    The extracted output will be written in output file.

-tbp total-bp-number, --total-bp total-bp-number
                    Total number of basepair in DNA/RNA.
                    It is an essential input.

-bins bins, --bins bins
                     Number of bins in the histogram
                    Default value is 30.

-p parameter, --parameter parameter
                    Parameter name.
                    This parameter will be extracted from file. Ensure that parameter is present
                    in the file, otherwise wrong values will be extracted from file.

-bs bp/s-start-number, --bp-start bp/s-start-number
                    First BP/BPS of DNA after which parameter will be extracted.
                    If it is not given, first basepair or base-step will be considered.

-be bp/s-end-number, --bp-end bp/s-end-number
                    Last BP/BPS of DNA upto which parameter will be extracted.

                    If it is not given, parameter for only a single bp/s given with -bs/--bp-start
                    option will be extracted.

-mm sum-or-mean, --merge-method sum-or-mean
                    Method to merge the parameter of a DNA segment from local parameters
                    of all base-pairs/steps that are within the range given by '-bs' and '-be'.

                    Currently accepted keywords are as follows:
                        * mean : Average of local parameters
                        * sum : Sum of local parameters

                    When only "-bs" option is provided without "-be", then -mm/--merge-method is
                    not required.

-fbp 1, --first-bp 1  Basepair number of first base-pair.
                    Usually it is one. Therefore, if this option is not provided, base-pair
                    numbering will start from one.

                    In rare cases, base-pair numbering might start with other number. In those
                    cases, use this option to start numbering of basepair from other number than


dnaMD histogram -i pdna.h5 -o histogram.dat -tbp 60 -bs 20 -be 45 -p rise -mm sum -bins 20

Following output is obtained in histogram.dat file.

# "rise"     Density
84.082      0.0
84.278      0.00509694
84.474      0.0
84.67       0.00509694
84.866      0.00509694
85.062      0.0203878
85.258      0.0356786
85.454      0.107036
85.65       0.0560664

It can be plotted by xmgrace as following:

xmgrace histogram.dat

The obtained plot is similar to the histogram plot shown here for 20-45 bp length bound DNA.