genconf rotation option not working properly
Created an attachment (id=338)
It seems that the rotation option of genconf is not working properly. It seems to shift the centers of mass of the original configurations.
Generating a box without the -rot option makes the problem easy to see.
1. Generate a box of 125 mols of tridecanol:
$ genbox -f tridecanol.gro -nbox 5 5 5 -o origbox.gro
2. Increase the box edges 4.10775 -> 7.3, which should account for any overlap between boxes ( 7.3 > sqrt(3)*4.10775 ).
3. Generate a simulation box consisting of 1000 mols of tridecanol
$ genbox -f supersizedbox.gro -nbox 2 2 2 -o big-norot.gro
The outcome is what one would expect - the cubes are nicely in a grid in the simulation box.
However, if you use the rotation option
$ genbox -f supersizedbox.gro -nbox 2 2 2 -seed 1 -rot -o big-rot.gro
you get something strange: overlapping boxes, and the grid order is no longer there.