[gmx-users] Removal of Waters in Hydrophobic Core

[Christopher Neale]

I have not run that in a long time, but looking at it (and my initial post here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-May/021526.html ) it seems like I wrote out the instructions incorrectly. Sorry about that!

In the post linked above, step 8 is:

cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro

but I think you would really want to do this:

cat not_last_line.gro keep_these_waters.gro last_line.gro > new_system.gro

where the change is to *actually use* the keep_these_waters.gro file that we create with the script ;)

Looks like I realized that a number of years ago: http://www.mail-archive.com/gmx-users@gromacs.org/msg37736.html

Sorry for the confusion, indeed the commands listed on the webpage seem like they should lead you to recover exactly the initial file :(

Note also that you need to set the upper and lower bounds correctly, and modify the script as noted if you are using a 4-point (or 5-ponit) water model, and make the noted change if your input file has also velocities. All of those things are correctly indicated on the webpage though.

Please reply back to this list if that change works for you as expected and I'll bring it to Mark's attention to see if he can update the webpage.
________________________________________
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: 26 November 2016 02:18:09
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Removal of Waters in Hydrophobic Core

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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