[gmx-users] output format of gromacs utilities

[Berk Hess]

Hi,

For many tools setting the environment variable
GMX_VIEW_XVG = xmgr
will work.

Berk


> Date: Mon, 22 Sep 2008 11:05:58 +0200
> From: jhub at gwdg.de
> To: vvchaban at gmail.com; gmx-users at gromacs.org
> Subject: Re: [gmx-users] output format of gromacs utilities
> CC: 
> 
> Vitaly Chaban wrote:
> > Hello,
> > 
> > In gromacs analysis tools, is it possible to output multiple data
> > columns as several 'parallel' columns (not as pairs delimited by '&')?
> 
> I don't think so, but i once wrote a script that does the transformation
> for you. Here it is.
> 
> Best, Jochen
> 
> 
> #!/bin/bash
> 
> tmpdir=xxxxx.tmp
> rm -fr $tmpdir
> mkdir $tmpdir
> 
> echo Removing comments...
> egrep -v '^@|^#' $1 > $tmpdir/xxx.tmp
> 
> here=`pwd`
> cd $tmpdir
> echo "Splitting $1 at &'s ..."
> csplit -n 5 --silent xxx.tmp '/&/' '{*}'
> grep '[0-9]' xx00000 | awk '{print $1}' > times.tmp
> 
> rm -f yy*[0-9]
> for i in xx[0-9][0-9][0-9][0-9][0-9]; do
>     nr=$(echo $i|tr -cd [:digit:])
>     if grep -q '[0-9]' $i; then
>         echo writing yy$nr ...
>         grep '[0-9]' $i | awk '{print $2}' > yy$nr
>     fi
> done
> 
> out=${1%%.xvg}.dat
> paste -d ' ' times.tmp yy[0-9][0-9][0-9][0-9][0-9] > $out
> echo created ${1%%.xvg}.dat
> 
> 
> > 
> > I experience difficulties to read such (xvg) format by sigmaplot.
> > 
> > 
> 
> 
> -- 
> ************************************************
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
> ************************************************
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