[gmx-users] Removal of Waters in Hydrophobic Core

[Sanim Rahman]

Thank you Chris,

I tried the commands and I was able to obtain an output
keep_these_waters.gro with about 3.5 MB of data. However, when I continued
with the rest of the commands:

tail -1 initial.gro > last_line.gro
head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 )
initial.gro > not_last_line.gro
cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
editconf -f new_system.gro -o new_system_sequential_numbers.gro

I still failed to obtain a new structure. The structure is the same as
solvated.gro. I am going to put extreme z-coordinates to see if all the
water molecules will be removed. Other than that, do you have any
suggestions?

*Sanim Rahman*
B.S. Chemical Engineering, 2019
Undergraduate Researcher, Global Center for Hearing and Speech Research



On Fri, Nov 25, 2016 at 3:48 PM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> not sure if it is a typo or perhaps a command structure I am unfamiliar
> with, but I don't understand your command.
>
> Try this:
>
> chmod +x keepbyz.pl
> ./keepbyz.pl new_waters.gro > keep_these_waters.gro
>
> see here: http://www.gromacs.org/Documentation/How-tos/
> Membrane_Simulations?highlight=generates
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sanim
> Rahman <sanimr at mail.usf.edu>
> Sent: 24 November 2016 16:12:11
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Removal of Waters in Hydrophobic Core
>
> Hello,
>
> I am currently working through the second tutorial of the Bevan Labs KALP15
> simulation. I am attempting to use the keepbyz.pl script to remove the
> waters in the hydrophobic core. I have designated a upperz and
> lowerz coordinated and followed the entire section highlighted in the
> instructions, however, my output (new_system_sequential_numbers.gro) has
> no
> deleted water molecules. It is the same system as  solvated.gro.
>
> I believe my error is within the keepbyz.pl file, because when I input the
> command:
>
> chmod +x keepbyz.pl new_waters.gro > keep_these_waters.gro
>
> the file "keep_these_waters.gro" is an empty file.
>
> Here is my script for keepbyz.pl:
>
> #!/bin/bash
> # give new_waters.gro as first command line arguement
> upperz=5.821
> lowerz=0.574
> 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
>
> I will appreciate the help!
>
> Regards,
>
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Resident Assistant, Castor Hall Engineering Living Learning Community
> 2016-2017
> Undergraduate Researcher, Global Center for Hearing and Speech Research
> Honors College Engineering Peer Advisor
> <https://www.linkedin.com/pub/sanim-rahman/108/a64/986>
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