AboutDownloadsDocumentsForumsWikiIssuesNews
Date:
2013-04-17 18:40
Priority:
3
State:
Open
Submitted by:
Mark Williamson (mjw)
Assigned to:
Nobody (None)
Summary:
System->addConstraint() should (at least) raise an exception for a duplicate constraint.

Detailed description
Having been testing out Modeller.loadHydrogenDefinitions() and Topology.loadBondDefinitions()in OpenMM5.1 beta, I stumbled upon a subtle problem, that was my own fault, but could have been resolved quicker with an exception being thrown.

To cut a very long story short and summarise three days of debugging, it turns out that a simulation will crash with a NaN if there is a duplicate term for a constraint. This was being caused by some bespoke parameters that had duplicate entries to those in amber99sb.xml. Serialising the system object and looking in the Constraints element revealed two entries for a particle:

<Constraint d=".101" p1="19" p2="20" />
....etc...
<Constraint d=".101" p1="19" p2="20" />

Removing these duplicates, deserialising, then proceeding with the simulation resolved the issue.

Even though this problem is caused by my faulty parameters, I still think System->addConstraint() should at least raise an exception if there is more than one entry for a given pair.

A wider issue, and out of scope for this bug, is whether an exception should be raised if one attempts to add a duplicate force to a system. I know NonbondedForce.addException() has an "replace" option, but I don't think other force objects have this ability.

Add A Comment: Notepad

Comments:

No Comments Have Been Posted

Attached Files:

Changes

No Changes Have Been Made to This Item

Feedback