Sorry, Ali, it's not really possible for me to simplify those commands. That's
about as simple as it gets.
I suggest that you start a normal post that follows the form: I did this (paste
commands) and I got this
(paste error message). Also, when you get a message like
Fatal error:
Invalid line in tmpgro.gro for atom 1:
1LI C1 1 0.8 1.9 0.7
it becomes interesting to know what the result of "head tmpgro.gro" is.
* Note that you will need to also use a modified version of trjconv (see my
post on trjconv -center centering by
max-min and not the actual center).
-- original message --
Dear Chris
I found your topic:
chris.neale | 21 Aug 01:30 , problem with g_density -center
The following text is your email. Is it correct?
I pursue your steps but :
1- I don't understand first commands that related to directories and :
empty.mdp ? and command : avg=($(cat coord.xvg|grep -v '[@|#]' |
awk '{x+=$2;y+=$3;z+=$4;n++}
END{print -1*x/n,-1*y/n}'))
2- I encounter with a problem in now make a new .tpr file, my error:
Fatal error:
Invalid line in tmpgro.gro for atom 1:
1LI C1 1 0.8 1.9 0.7
my top file is the same first top file in my simulation,
3- You can help me by simpler commands?
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