Great, thank you very much, will try it out,
chris.neale at utoronto.ca wrote:
> If I have a solvated membrane and I want to extend the z dimension and add new
> waters there, this is what I do. The script could be modified to get rid of new
> waters in any x/y/z dimensions (around line 41 of the script).
>
> 1. run genbox on initial.gro to create solvated.gro
> 2. cp solvated.gro new_waters.gro
> 3. use vi to remove everything in new_waters.gro except the new waters (make
> sure you remove waters that were in initial.gro)
> 4. use vi to edit keepbyz.pl
> - upperz and lowerz variables as you please
> - sol to the name of your solvent molecule
> 5. run keepbyz.pl on new_waters.gro
> ./keepbyz new_waters.gro > keep_these_waters.gro
> 6. tail -1 initial.gro > last_line.gro
> 7. head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 ) initial.gro
>
>> not_last_line.gro
>>
> 8. cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
> 9. editconf -f new_system.gro -o new_system_sequential_numbers.gro
>
> Here is the script (make sure you chmod +x keepbyz.pl):
>
> #!/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)
> 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
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