Seth Axen
Seth Axen
It would probably be good to understand the set of use cases this feature is intended to address. For example, with an atomic resolution system restrained with a CHARMM forcefield...
@benmwebb do you have any idea why ctest doesn't find the tests?
@benmwebb thanks for the changes. Is this now superseded by the `ci.yml` workflow in the default branch?
> Something in the nose environment doesn't look quite right yet though (probably because it's trying to run everything in one process, and the tests weren't written with that in...
@benmwebb: > This assumes that rigid bodies do not overlap, are not nested, and do not contain any non-rigid members Nesting doesn't seem too difficult to handle, but do you...
Also, can rigid bodies overlap in IMP?
@benmwebb do you have more details on Modeller's implementation of rigid body MD linked to above? The documentation is not explicit regarding how the equations of motion wrt the rotational...
> If you're worried about integrator error in your MD code, IMP is probably the wrong tool for you... but I don't have any particular attachment to Verlet integration. Note...
It turns out that the propagation of derivatives and torques requires no assumptions regarding the nature of the reference frame (the coordinates don't need to be the COM). The COM...
I'll look at this more closely later, but I think here with SVD we have the same problem we have with the eigendecomposition. Namely, when singular values are exactly non-unique,...