#!/bin/bash
#  Convert configuration from xyz format to gromacs format (*.gro).
#    By Ulf R. Pedersen (www.urp.dk), June 2011.

if [ $# != 4 ]; then
   echo "Convert configuration from xyz-format to gromacs format (*.gro)."
   echo "Usage: $0 <filename of xyz-file> <X box length> <Y box length> <Z box length>"
   exit 1
fi

xyzFile=$1
groFile=$1.gro

# Read box lengths
X=$2
Y=$3
Z=$4

# Copy comment line from xyz-file to gro-file
head -n 2 $xyzFile | tail -n 1 > $groFile

# Write number of particles
echo `head -n 1 $xyzFile` >> $groFile

# Print coordinates
awk '{if(NR>2){printf "%5i%5s%5s%5s%8.3f%8.3f%8.3f\n",NR-2,"atm",$1,NR-2,$2,$3,$4}}' $xyzFile  >> $groFile

# Add box lengths
echo $X $Y $Z >> $groFile