put logs to logs directory + -p for the mkdir commands

diff --git a/runmd b/runmd
index d50d9ae..541734b 100755 (executable)
--- a/runmd
+++ b/runmd
@@ -8,13 +8,14 @@ if [ ! -f ./config ]; then
        exit
 fi
 
-[ ! -d $1 ] && mkdir $1
+[ ! -d $1 ] && mkdir -p $1
 
 ./clean $1
 
 cp -v config $1/config
 
-time ./mdrun -c ./config -s $1
+mkdir -p logs
+time ./mdrun -c ./config -s $1 | tee logs/run_`basename $1`.log
 
 if [ "$?" == "0" ]; then
        #./perms
@@ -24,7 +25,7 @@ if [ "$?" == "0" ]; then
 
                # center unit cell
                ./visualize -w 640 -h 480 -d $1 \
-                           -nll -0.56 -0.56 -0.56 -fur 0.56 0.56 0.56 \
+                           -nll -0.56 -0.56 -0.76 -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