[gmx-users] water segment in the z-direction

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Feb 3 14:44:34 CET 2011

Dear Tusar:

Let's keep this on the mailing list.

You could learn about expr with a simple google search! It should have  
worked though, did you mangle the command somehow when you typed it?  
There should be " > not_last_line.gro" with a redirect at the end but  
you have only a star. Nevertheless, my scripting has improved a bit  
since I wrote that and you could replace 7 by:

head -n -1 initial.gro > not_last_line.gro

And, to answer your second question, you use keep_these_waters.gro in  
part 8, along with other files, to create new_system.gro


-- original message --

I am trying to increase the size of the water segment in the z-direction.
For this purpose I am following your recommended steps and 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 )  
* 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  

I could successfully go through steps 1 to 6. However, I am unable to
execute step 7. In particular, what is "expr" in step7? Moreover, The file,

keep_these_waters.gro" that I have generated in step 5, where do I use
it subsequently?

I shall remain obliged for your kind answer.
Best Regards.

Dr. Tusar Bandyopadhyay
Theoretical Chemistry Section,
Chemistry Group
BARC, Trombay

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