[gmx-users] problem with g_density -center

[Christopher Neale]

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?