Parameter as a function of time

This can be used to extract the parameter of either a specific base-pair/step or over a DNA segment as a function of time.


usage: dnaMD vsTime [-h] [-i L-BP_cdna.dat] [-o output.dat]
                [-tbp total-bp-number] [-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.

-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 vsTime -i fdna.h5 -tbp 60 -bs 10 -be 50 -p "curvature" -mm sum -o curv.dat

Following output is obtained in curv.dat file.

# Time       "curvature"
0.0 0.14487306619300122
100.0       0.24987540226819524
200.0       0.19187540226819527
300.0       0.20787540226819526
400.0       0.26187540226819517
500.0       0.24582073103934177
600.0       0.23887540226819526
700.0       0.2478754022681953
800.0       0.2558754022681952

It can be plotted by xmgrace as following:

xmgrace curv.dat

The obtained plot is similar to the curvature plot shown here for 10-50 bp length.