Average parameters as a function of base-pair/step

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


usage: dnaMD vsBPS [-h] [-i L-BP_cdna.dat] [-o output.dat]
                   [-tbp total-bp-number] [-p parameter] [-em block]
                   [-mb bp/s number] [-gt g_analyze] [-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.

-em block, --error-method block
                       Error method
                      It can be as following:
                      * "acf": Using autocorrelation function to determine autocoprrelation time and used as time
                               to get the independent frame.
                      * "block": Block averaging error
                      * "std": standard deviation

                      In case of "acf" and "block", gromacs tool "g_analyze" or "gmx analyze" will be used. Either
                      of these tools should be in path for error calculation.

-mb bp/s number, --merge-bps bp/s number
                      Number of consecutive base-pairs/steps to merge for creating the small non-overlapping DNA
                      segments. By default, averages and errors are calculated for each base-pair/step separately.
                      However, averages  and errors can also  be calculated for small non-overlapping DNA segment
                      by merging the parameters of consecutive base-pairs/steps.

-gt g_analyze, --gromacs-tool g_analyze
                      Tools to calculate autocorrelation time or bloack averaging error.
                      By default it is g_analyze (Gromacs-4.5.x/4.6.x versions). For newer versions, use "gmx analyze".

-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, last basepair or base-step will be considered.

-mm sum-or-mean, --merge-method sum-or-mean
                      Method to merge the parameters of consecutive basepairs/steps given by -mb/--merge-bps.

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

-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 vsBPS -i fdna.h5 -o vsBPS.dat -tbp 60 -bs 5 -be 56 -p rise -mm sum -mb 4 -gt "gmx analyze" -em block

Following output is obtained in vsBPS.dat file.

# bp(mid)    rise-avg        rise-error
7                13.313      0.0161982
11               13.5327     0.0174155
15               13.5497     0.0191224
19               13.376      0.0778458
23               13.5107     0.0167237
27               13.6694     0.0254001
31               13.5624     0.0178427

It can be plotted by xmgrace as following:

xmgrace -settype xydy vsBPS.dat

The obtained plot is similar to the second plot shown here for bound DNA.