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Bug #277

genconf rotation option not working properly

Added by Jussi Lehtola almost 11 years ago. Updated almost 11 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Created an attachment (id=338)
Original box

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.

origbox.gro (231 KB) origbox.gro Original box Jussi Lehtola, 01/15/2009 04:49 PM
supersizedbox.gro (231 KB) supersizedbox.gro Box with edge lengths increased to prevent overlap Jussi Lehtola, 01/15/2009 04:50 PM
big-norot.gro (2.76 MB) big-norot.gro Simulation box generated without the -rot option Jussi Lehtola, 01/15/2009 04:50 PM
big-rot.gro (2.76 MB) big-rot.gro Simulation box generated with the -rot option demonstrating unwanted behaviour Jussi Lehtola, 01/15/2009 04:51 PM

History

#1 Updated by Jussi Lehtola almost 11 years ago

Created an attachment (id=339)
Box with edge lengths increased to prevent overlap

#2 Updated by Jussi Lehtola almost 11 years ago

Created an attachment (id=340)
Simulation box generated without the -rot option

#3 Updated by Jussi Lehtola almost 11 years ago

Created an attachment (id=341)
Simulation box generated with the -rot option demonstrating unwanted behaviour

#4 Updated by Jussi Lehtola almost 11 years ago

I'm using Gromacs 4.0.2 (which seems to be missing from Bugzilla).

#5 Updated by Berk Hess almost 11 years ago

There were two bugs that affected the origin of the rotation.
I fixed them both.

Also -maxrot was 90 by default, rotating between 0 and 90 degrees.
Now -maxrot is 180 by default, rotating between -180 and 180 degrees.

Berk

#6 Updated by Jussi Lehtola almost 11 years ago

OK, thanks, it seems to work now.

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