plotXVG: Plot time series from GROMACS XVG files
In Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences
plotXVG R Documentation
Plot time series from GROMACS XVG files
Description
Read and plot output data from a XVG format file.
Usage
plotXVG(XVGfile, ...)
Arguments
XVGfile
A .XVG output file of the GROMACS molecular dynamics package
...
Arguments to be passed to methods, such as graphical parameters.
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 <jpaezpae@purdue.edu>
Original: Daniel Osorio <dcosorioh@unal.edu.co>
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
XVGfile <- system.file("xvg-files/epot.xvg",package="Peptides")
plotXVG(XVGfile)
Peptides documentation built on May 31, 2023, 9:47 p.m.
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| plotXVG | R Documentation |
Plot time series from GROMACS XVG files
Description
Read and plot output data from a XVG format file.
Usage
plotXVG(XVGfile, ...)
Arguments
XVGfile |
A .XVG output file of the GROMACS molecular dynamics package |
... |
Arguments to be passed to methods, such as graphical parameters. |
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 <jpaezpae@purdue.edu>
Original: Daniel Osorio <dcosorioh@unal.edu.co>
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
XVGfile <- system.file("xvg-files/epot.xvg",package="Peptides")
plotXVG(XVGfile)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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