minim.sh

#!/bin/bash

np=$1
box=${2:-1.0}

[ -z "$gmx" ] && gmx="/work/gmx-docker --"

if [ -z "$np" ]; then
	echo usage: $0 number_of_cores
	exit 1
fi

unset OMP_NUM_THREADS


minone() {
	in=$1
	
	base=$(basename $in .pdb)
	
#	echo Prepare topology
	$gmx pdb2gmx -f $base.pdb -o $base.gro -p $base -i $base -water spce -ff amber99 -ignh &&
#	echo Add box
	$gmx editconf -f $base.gro -o $base-box.gro -d $box -bt cubic &&
	# not solvating
	# no ions
#	echo Minimize
	$gmx grompp -f minim.mdp -c $base-box.gro -p $base.top -o $base-min.tpr -po $base-min.mdp -maxwarn 1 &&
	$gmx mdrun -v -deffnm $base-min -ntomp 1 &&
	(echo 10; echo) | $gmx energy -f $base-min.edr -xvg none -o $base.xvg &&
	tail -1 $base.xvg >$base.minen && rm $base.xvg
}

nfil=$(ls conf*.pdb | wc -l)

echo Starting $np parallel processes 
for p in $(seq 1 $np); do
	(
		i=$p
		while [ $i -le $nfil ]; do
			minone conf$i.pdb
			i=$(($i + $np))
		done
	) >minim-$p.log 2>&1 &
done

echo Waiting for workers to finish 
wait

echo Done, last 200 lines of their logs
echo

for p in $(seq 1 $np); do
	echo ----- $p -----
	tail -200 minim-$p.log
done