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
Chris.
-- 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 )
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
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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