[gmx-users] g_sorient HELP!!!

Berk Hess gmx3 at hotmail.com
Tue Oct 28 11:35:02 CET 2003

>Hello All
>I great a gro file that looks like this
>     1ARR    ARR    1   1.750   2.500   2.500  0.0000  0.0000  0.0000
>     2SOL     OW    2   1.850   2.500   2.500  0.6290  0.3015 -0.0304
>     2SOL    HW1    3   1.900   2.550   2.500  0.8230 -0.5734  2.1610
>     2SOL    HW2    4   1.900   2.450   2.500  -0.2208  2.6625 -0.1271
>Then I run
>g_soreint -f test -s test.gro

I have found three bugs in g_sorient:

One is that even when -com has not been specified it calculates
the com of one particle, but with a gro or pdb file for -s the masses
have not been loaded. This explains the nan's in your output.
Using a tpr file for -s would circumvent this.

Another is that in the -o output the histogram has always been shifted
one bin to right. So even if you have masses you would get 0 in the
case of your gro file, as the angle is 180 and this shifts out on the right
side of the histogram. (All the other output files are correct)

Yet another bug is that -com just uses the coordinates of the first
particle in the group instead of the com of the group.

All these bugs have been fixed for the new release.


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