readXVG: Read output data from a XVG format file.

In Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Read output data from a XVG format file.

Description

XVG is the default format file of the GROMACS molecular dynamics package, contains data formatted to be imported into the Grace 2-D plotting program.

Usage

readXVG(file)

Arguments

file	A .XVG output file of the GROMACS molecular dynamics package

Details

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package designed for simulations of proteins, lipids and nucleic acids. It is free, open source software released under the GNU General Public License. The file format used by GROMACS is XVG. This format can be displayed in graphical form through the GRACE program on UNIX/LINUX systems and the GNUPlot program on Windows. XVG files are plain text files containing tabular data separated by tabulators and two types of comments which contain data labels. Although manual editing is possible, this is not a viable option when working with multiple files of this type. For ease of reading, information management and data plotting, the functions read.xvg and plot.xvg were incorporated.

Author(s)

Latest: J. Sebastian Paez <[e-mail]> and hongbo-zhu-cn <@github>

Original: Daniel Osorio <[e-mail]>

References

Pronk, S., Pall, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., ... & Lindahl, E. (2013). GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29 (7), 845-854.

Examples

# READING FILE
XVGfile <- system.file("xvg-files/epot.xvg",package="Peptides")
readXVG(XVGfile)

#    Time (ps)  Potential
#  1         1 6672471040
#  2         2 6516461568
#  3         3 6351947264
#  4         4 6183133184
#  5         5 6015310336
#  6         6 5854271488

Peptides documentation built on May 29, 2024, 11:02 a.m.