msmbuilder-legacy
msmbuilder-legacy copied to clipboard
msmbuilder
Legacy release of MSMBuilder
I am using SaveStructures for making a movie from MSM. I have list of states using the sample function from MSMLib.msm_analysis and I want the xtc which contains the states...
CalculateImpliedTimscales.py gives errors when running on Tutorial data. Digging into the code, the error stems from MSMLib.py class Reversible_MLE_Estimator. The logger at line 1238 in MSMLib.py throws the error. Looking...
... application of AtomIndices.dat Generators were mistakenly screened with AtomIndices.dat, when all atoms from generators should be used. This fix sets the atom indices attribute to the 'metric' object to...
This is to give people a feel for the interface. At this point, mcmc.TransitionSampler and mcmc.RateSampler are working.
Is there an option for this? It would be very helpful. Thanks!
So if you do this: ``` Cluster.py rmsd kcenters -k 50 Assign.py rmsd ``` You end up with a totally arcane error: ``` {'generators': 'Data/Gens.h5', 'metric': 'rmsd', 'output_dir': 'Data/', 'project':...
BuildMSM.py prints: 14:00:58 - Selected component 387 with population 0.993999 . . . 14:02:45 - Ergodic trimming discarded: 0.589649 percent of your data The first number is the raw population...
Hi, After using 'BuildMSM.py', a macro-state network is obtained. Let's say 100-node network.I am wondering how to extract the centroid structures. Or is there a built-in function which calculates the...
Hi, everyone I'm working with my system using msmbuilder2.8.2. The cluster process has succeed with the commond " msmb Cluster rmsd hybrid -d 0.045 -l 50" . But the command...
Tiny issue, but often cysteines are deprotonated (like when coordinating zinc in my case). In AMBER, at least, the name for these residues are CYM, but CreateAtomIndices.py just ignored them...
