Inconsistent graph PBC results with monomers connected by restraints - Redmine #2549
The graph code implicitly assumes that the bonded interactions
connecting atoms in a moleculetype a short-ranged compared to the box
size. But this is not necessarily the case when multiple monomers in a
single moleculetype are connected by restraints. Such restraints can
work over more than half the box length. In the current code this can
lead to monomers being broken over PBC.
The least we should do is add a check for this, but this might be
computationally expensive and/or complicated. The solution for the user
would then be to increase the box size.
Ideally we would want a solution, but that can only be done through
allowing the user to specify how the monomers should be connected.
(from redmine: issue id 2549, created on 2018-06-07 by berkhess, closed on 2018-09-04)
- Changesets:
- Revision 0ef40b73 by Berk Hess on 2018-06-12T08:13:56Z:
Add fatal error for inconsistent graph
In case a moleculetype consists of multiple monomers connected
by restraints, an inconsistent graph could be generated.
Now a fatal error with explanation is generated for such cases.
Also a fatal error is generated with an inconsistent graph with long
bonds in general.
Fixes #2549
Change-Id: I6fa11fb7cefd74ed077c1fb523a2147c91e0d0fd