PyEMMA

PyEMMA copied to clipboard

How to deal with many short trajectories

4

I have like 30 short MD runs each of which is 50-100ns long. I would like to build MSM using these set of trajectories. Should I concatenate the trajectories before...

KrishnenduSinha12

Tips on combining features across systems

6

Hello, I have two systems, A and B. The only differences between the two are a few point mutations. After much analysis of the MD trajectories, I can say that...

cgseitz

Is TRAM appropriate in this setting?

5

Hello, I am constructing MSMs to get a coarse grained representation of my system's dynamics at various values of the system parameters; in this case, temperature. I have constructed an...

onehalfatsquared

Could not allocate enough memory to map all data

3

Hello, I am trying to find out vamp score for different features, When I am adding the features based on the heavy atom distances in the protein. I got following...

rubinanoor9

pyemma.util no attribute 'context'

4

Hi, I installed pyEMMA (2.5.11) with pip. I tried the test case described here http://emma-project.org/latest/tutorials/notebooks/00-pentapeptide-showcase.html#Feature-selection with my own Gromacs trajectory. Then, I get the error message: AttributeError: module 'pyemma.util' has...

pojeda

_bar_df wrong for loop boundary

3

In PyEMMA/pyemma/thermo/extensions/bar/_bar.c The second for loop should run from 0 to `L2`, not `L1`. Current implementation gives an access violation whenever `L1` > `L2` ```python extern double _bar_df(double *db_IJ, int...

MaaikeG

Expose minRMSD metric directly

2

instead of importing it implicitly upon construction of clustering estimators

clonker

Make data sources compatible to deeptime

2

clonker

Issue deprecation warnings

2

- [x] for coordinates package (#1557) - [ ] for MSM package - [ ] for TRAM and dTRAM in thermo package - [x] for plotting package where appropriate What...

clonker

Examples how to migrate code from current PyEMMA API to deeptime

1

- [ ] for coordinates package - [ ] for msm package - [ ] for thermo package

clonker