vsBPS
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:
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
one.
Example
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.