Dear all users,
I am using tutorial Kalp15 in DPPC from Justin's tutorials.I want to remove
waters which are between bilayers so I use this script:
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
#!/bin/bash
# give x.gro as first command line arguement
upperz=6.417
lowerz=0.820
sol=SOL
count=0
cat $1 | grep "$sol" | while read line; do
for first in $line; do
break
done
if [ "$count" = 3 ]; then
count=0
fi
count=$(expr $count + 1)
if [ "$count" != 1 ]; then
continue
fi
l=${#line}
m=$(expr $l - 24) // would use -48 if velocities are also in .gro and -24
otherwise
i=1
for word in ${line:$m}; do
if [ "$i" = 1 ]; then
popex=$word
else
if [ "$i" = 2 ]; then
popey=$word
else
if [ "$i" = 3 ]; then
popez=$word
break
fi
fi
fi
i=$(expr $i + 1)
done
nolx=`echo "$popez > $upperz" | bc`
nohx=`echo "$popez < $lowerz" | bc`
myno=$(expr $nolx + $nohx)
if [ "$myno" != 0 ]; then
z=${#first}
if [ "$z" != 8 ]; then
sfirst="[[:space:]]$first"
else
sfirst=$first
fi
`echo grep $sfirst $1`
fi
done
the original file has 2626 molecule of water but after ruuning this command,
just the file has 24 molecules of water :
./keepbyz.sh new_waters.gro > keep_these_waters.gro
Here is my question:why is this command deletes 2602 molecules of water while
2626 molecules all are in box?and how can I understand that this command runs
correctly?
Thanks in advanced,Negar
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