As detailed below, I have three issues (two coding-related, one science-related) regarding the implementation of the AmoebaMultipoleForce and its xml force field interface. For context, I'm trying to develop force field that contains both induced dipoles and permanent multipoles, and am currently in...

As this post may have been missed, and because the segfaults are probably a bug, I moved the discussion over to the github issue tracker:

https://github.com/pandegroup/openmm/issues/1654

I'm in the process of putting together a force field that uses both AmoebaMultipoleForce and CustomHbondForce, and experiencing sporadic segmentation faults. My test files are attached; the test in each subdirectory can be run with a $ bash submit_all.sh command, which *should* calculate the interac...

Peter, One last question on this topic (hopefully). I've started testing use of the CustomHbondForce, and, as a sanity check, wanted to make sure that CustomNonbondedForce and CustomHbondForce were giving me the same energies for simple energy expressions. I've copied my xml files and run scripts be...

Follow-up: If a print out the parameters for each of the acceptor and donor pairs, I get the following: 3_donor_2_acceptor num acceptors: 12 Acceptor parameters (a1,a2,a3,params): [0, 1, -1, (115.0, 0.2)] [1, 2, -1, (115.0, 0.2)] [2, 3, -1, (115.0, 0.2)] [3, 4, -1, (115.0, 0.2)] [4, 5, -1, (115.0, 0...

Peter, All of my example test cases now run without crashing, and the number of acceptor/donor particles is correct. I still think there's a bug in the code whereby the acceptor/donor labels don't match between the energy expression (a1, d1, etc.) and the Donor/Acceptor tag (class1, class2, etc.): T...

Peter, I didn't see your post until just now, so sorry for the delay. I've downloaded the changes and ran the example you listed in the documentation; that particular example works fine for me. However, I notice a couple of bugs (either that or I'm doing something wrong) when using different combina...

I can't think of an exception either to the strategy you mentioned, and I imagine that requiring bonded acceptor and donor groups would allow you to use a nearly-identical set-up as CustomAngleForce (except with Donor and Acceptor tags rather than Angle tags). Let me know if you plan to add this in ...

I'm looking to use CustomHbondForce in my force fields. For consistency, I would prefer to add a CustomHbondForce tag to a pre-existing xml file that describes the other forces present in my force field. Looking at the documentation, http://docs.openmm.org/7.0.0/userguide/application.html#writing-th...

Peter,

Yes, this fixes my problem! As always, thank you so much for your timely help.

Cheers,
Mary