#!/bin/bash
#  Convert configuration from gromacs format (*.gro) to the xyz format
#    By Ulf R. Pedersen (www.urp.dk), May 2014.

if [ $# != 1 ]; then 
    echo "Convert configuration from gromacs format (*.gro) to the xyz format." 
    echo "Usage: $0 <filename of gromacs gro-file>" 
    exit 1 
fi 

groFile=$1
forename=`echo $groFile|awk -F. '{print $1}'`
xyzFile=$forename.xyz 

echo begin converting $groFile to $xyzFile

if [ ! -e $groFile  ];then
    echo "Error: the gromacs input file $groFile does not exist. Exit."
    exit 1
fi

if [ -e $xyzFile ];then
    echo "Error: the xyz output file $xyzFile already exist. Exit."
    exit 1
fi

# Number of particles in first line
N=`head -n 2 $groFile | tail -n 1`
echo $N > $xyzFile

# Comment in secound line
head -n 1 $groFile >> $xyzFile

# Coordinates
tail -n $(( $N + 1 )) $groFile | head -n $N | awk '{
    type=$2
    x=$4
    y=$5
    z=$6
    print type,x,y,z
}' >> $xyzFile

echo done converting $groFile to $xyzFile