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]
-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.
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
# 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.