[gmx-users] A simple XVG viewer
mglerner+gromacs at gmail.com
Thu Nov 5 16:29:42 CET 2009
On Thu, Nov 5, 2009 at 10:23 AM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> So, what's the advantage over using e.g. (xm)grace?
I'm not sure. The last time I tried, xmgrace refused to install on my Mac.
This certainly isn't a big analysis/plotting package. It's just a quick way
to step through XVG files.
> Michael Lerner skrev:
>> (My apologies if this shows up several times. I sent it yesterday, but it
>> appears that it won't go through to the list if I include a screenshot.)
>> I wanted a quick way to plot the data in XVG files, so I wrote a quick
>> little GUI viewer in Python this morning. You point it at an XVG file and it
>> pops up a GUI where you can click buttons to step through the columns of
>> data, plot individual columns from the XVG file, or make a plot of
>> everything in the XVG file.
>> This makes it easy to dump all the information from an .edr/trr/xtc/etc
>> file and step through it visually in 30 seconds. That, in turn, makes me way
>> more likely to look at as much information as possible as part of my normal
>> I've only tested this on a few of my own XVG files, so it's possible that
>> my simple XVG parser doesn't cover everything.
>> Here's the help output. Let me know if anyone finds it useful.
>> Michael-Lerners-MacBook-Pro-2: ~ mglerner$ ./xvgviewer.py --help
>> Usage: Just a simple XVG viewer.
>> For each column in the XVG file, we plot
>> - the raw data (light blue)
>> - a running average (black)
>> - block averages (green)
>> We also print out
>> - the average over the simulation
>> - standard error over the blocks
>> - average of the standard deviations within each block
>> Block length is reported in number of frames, and its meaning will
>> therefore depend on the settings in your .mdp file as well as the
>> arguments you used when making the .xvg file.
>> We attempt to get units out of the XVG file, and we convert times to
>> nanoseconds before plotting.
>> This program requires
>> - Python 2.5 or 2.6
>> - wxPython 184.108.40.206+ (http://www.wxpython.org/)
>> - numpy 1.3.0+ (http://numpy.scipy.org/)
>> - matplotlib 0.99.0+ (http://matplotlib.sourceforge.net/)
>> - traits 3.2.0+ (http://code.enthought.com/projects/traits/)
>> All of which will be installed for you if you use the Enthought Python
>> Distribution (http://enthought.com/).
>> I mostly wrote this as a quick way to figure out how to use the Traits
>> GUI, but feel free to email me (m g lerner atsign gmail dot com) if
>> you have any questions.
>> -h, --help show this help message and exit
>> -f FILE, --file=FILE The XVG file [default energy.xvg]
>> Michael Lerner, Ph.D.
>> IRTA Postdoctoral Fellow
>> Laboratory of Computational Biology NIH/NHLBI
>> 5635 Fishers Lane, Room T909, MSC 9314
>> Rockville, MD 20852 (UPS/FedEx/Reality)
>> Bethesda MD 20892-9314 (USPS)
>> gmx-users mailing list gmx-users at gromacs.org
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> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 4537 fax: +46 18 511 755
> erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
> gmx-users mailing list gmx-users at gromacs.org
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Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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