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1 if [ -z "$1" ]; then
2         exit
3 fi
4
5 if [ ! -f ./config ]; then
6         exit
7 fi
8
9 [ ! -d $1 ] && mkdir $1
10
11 ./clean $1
12
13 cp -v config $1/config
14
15 # create run file
16 rf=`basename $1`
17 cat > run_$rf <<-EOF
18 #!/bin/bash
19 #$ -cwd
20
21 ./mdrun -c ./config -s $1
22
23 EOF
24
25 # submit job
26 qsub run_$rf
27
28 if [ "$?" == "0" ]; then
29         #./perms
30         if [ "$1" ] ; then
31                 # whole simulation cell
32                 #./visualize -w 640 -h 480 -d $1
33
34                 # center unit cell
35                 #./visualize -w 640 -h 480 -d $1 \
36                 #            -nll -2.4 -2.4 -2.4 -fur 3.8 3.8 3.8 \
37                 #           -b -2.03 -2.03 -2.03 3.39 3.39 3.39 \
38                 #           -r 0.6 -c 0.5 -11.0 2.5 -B 0.1
39
40                 # old rasmol
41                 #rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
42                 #./ppm2avi $1
43         fi
44 fi