+if [ -z "$1" ]; then
+ echo "specify a directory for logging and save files"
+ exit
+fi
+
+if [ ! -f ./config ]; then
+ echo "no config file found"
+ exit
+fi
+
+[ ! -d $1 ] && mkdir $1
+
+./clean $1
+
+./mdrun -c ./config -s $1
+
+if [ "$?" == "0" ]; then
+ #./perms
+ if [ "$1" ] ; then
+ # whole simulation cell
+ #./visualize -w 640 -h 480 -d $1
+
+ # center unit cell
+ ./visualize -w 640 -h 480 -d $1 \
+ -nll -0.56 -0.56 -0.56 -fur 0.56 0.56 0.56 \
+ -b -0.5 -0.5 -0.5 0.5 0.5 0.5 \
+ -c -0.2 -2.0 0.6 -L 0 0 -0.1 \
+ -r 0.6 -B 0.1
+
+ # old rasmol
+ #rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
+ ./ppm2avi $1
+
+ # copy config
+ cp -v config $1/config
+ fi
+fi