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get_cops_norm
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get_cops_norm
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#!/bin/bash
# Calculate order parameters for a dcd trajectory and store them
#
# Usage: get_cops_norm <name of dcd file> <stride>
if test -z "$2"
then
echo "Usage: get_cops_norm <name of dcd file> <stride>"
exit
fi
# Hard-coded stuff
source /home/jsavi/OPENV/bin/activate
psffile='/home/jsavi/cliu/acn_solvent/getOPs2/1.pdb'
mmpfile='/home/jsavi/cliu/acn_solvent/acn.mmp'
xtpfile='/home/jsavi/cliu/acn_solvent/acn_box6.xtp'
options='-numcells 0 -sfw 0.1 -cutoff 6.0'
dcdfile=$1
stride=$2
catdcd='/usr/local/lib/vmd/plugins/LINUXAMD64/bin/catdcd5.2/catdcd'
copcalc='/home/jsavi/GeneralOPs/copcalc/bin/copcalc'
numframes=`$catdcd -num $dcdfile | grep "Total frames" | cut -d' ' -f3`
thisdir=`pwd`
:> copfiles
mkdir -p copsnorm
mkdir -p cops
frame=1
function runcops(){
echo 'frame number is:' $frame
$catdcd -o cops/$frame.pdb -otype pdb -s $psffile -stype pdb -first $frame \
-last $frame -dcd $dcdfile
echo $frame 'catdcd done'
$copcalc -pdb cops/$frame.pdb -mmp $mmpfile -xtp $xtpfile -cop cops/$frame.cop \
$options
echo $frame 'cop done'
python3 /home/jsavi/cliu/acn_solvent/getOPs2/opnormalize.py --frame cops/$frame.pdb --origin 0 --atomspermol 6 --nmols 3200 \
--cutoff 6.0 --cop cops/$frame.cop --copnorm copsnorm/$frame.cop
echo $frame 'python done'
rm cops/$frame.pdb
echo "$thisdir/cops/$frame.cop" >> copfiles
frame=$(($frame+$stride))
}
#while [ $frame -le $numframes ]; do
# runcops $frame &
#done
#wait
for frame in $(seq 1 $numframes)
do
sem 10
runcops $frame &
done
sem --wait