trjconv does not recognize periodic molecules
Running trjconv on a periodic molecule yields
There were 4 inconsistent shifts. Check your topology
despite the tpr file knowing about this.
This obviously never worked and therefore this is a feature request rather than a bug.
#1 Updated by Berk Hess about 4 years ago
- Tracker changed from Feature to Bug
- Affected version set to 4.6
This is a bug. The pbc is read from the tpr and you should not be able to make a graph with periodic molecules. This used to work, but I see now that the (new, but by now old) rmpbc.cpp file never gets the inputrec passed.
Note that the only thing we need to add is a fatal error. This is trivial to do in gmx_trjconv.cpp. But it would be better to do it in rmpbc, because otherwise other tools might have the same issue.
#3 Updated by Berk Hess about 4 years ago
I don't understand your last comment. Calling rmpbc on a periodic molecule should result in a fatal error. The "solution" is not to ask for molecules to be made whole. Or are there cases where you get useful output from an operation that includes rmpbc?
Note that I set the affected version to 4.6. I left the target at 2016.