Did you compile OpenMM from source? If so, what version of `swig` did you use?

I've updated the script builder (see https://github.com/rmcgibbo/openmm-webbuilder/issues/8) to issue a warning in this scenario.

Just to throw this out there, I agree w/ Justin that it would be really nice if it were possible for all of the plugin code, including stuff for the python wrappers and CMAKE stuff, to be containing within a single directory. I'm not sure how feasible this is for a CMake though.

-Robert

We've set up an email list for users of msmbuilder. If you use msmbuilder, please sign up. This will be a convenient place for people inside and outside of the Pande group to ask and answer questions about using msmbuilder and building models. You can sign up with this link: https://mailman.stanford...

Ali, My first reaction is that a lag time of 1ps seems much to short for a large protein like barnase. We're in a very different regime here -- 110 resides -- than we are with the alanine dipeptide tutorial. Did you subsample further? Did both PCCA and PCCA+ have the eigenvalue convergence issue? Al...

Shan, That error message means that the model produced only has two states, and as such cannot have 10 timescales -- each timescale corresponds to an eigenvector of the transition matrix and a 2x2 matrix can only have 2 linearly independent eigenvectors. This is probably being caused by the ergodic ...

Lizhe, This looks like a shape error. Perhaps your assignments array 1 dimensional instead of the required 2 dimensional? We (the developers) have been trying to improve the quality of the error messages in the 2.6 release. Also, sorry for not checking this forum for a very long time. Please sign up...

Junyan, This is probably just statistical noise. The more clusters you have, the fewer number of transitions there are per pair of states, the the higher variance we should expect any statistical estimators to be. Also, sorry for not checking this forum for a very long time. Please sign up for the m...

The MSMBuilder development team is now using GitHub to host code and coordinate development activity. The repository is publicly accessible at https://github.com/SimTk/msmbuilder That site is now the main venues through which the developers are communicating and planning new features (and fixing bug...

Thanks for the bug report! No, you're not missing anything -- this is just a bug on our end. If you remove that line in the source code for the script (in scripts/CalculatePairwiseRMSD.py) and then reinstall the package, it should work. As you can see from grepping the source, the HierarchicalCluste...