Pedro Ojeda

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...

using non-public structures

1

Hi, I wonder if there is some feature in Alphafold to use structures that are not in public databases yet.

Hi, Would you mind taking a look at the suggested optimization? I extended the parallel region to include a reduction. /Pedro

2020-09-15-deep-learning-flux tutorial crashes

2

Hi, I tried the tutorial on this repo that is mentioned in the title. I am using Julia v. 1.8.5, and [052768ef] CUDA v4.0.1 [587475ba] Flux v0.13.12 [eb30cadb] MLDatasets v0.7.9...

Example/tutorial for dealing with MD trajectories

1

Hi, I have been exploring the documentation of Deeptime and I haven't found any example for dealing with MD trajectories from common packages like AMBER, GROMACS, NAMD, etc. PyEMMA was...

support for CUDA/11.7.0

2

Hi, I wonder if there are some guidelines to build ASE_INI with CUDA/11.7.0 and python 3.9.6? CUDA 9 is not longer supported in our HPC center. Thanks.

Hi, I have done the setup suggested in the Readme file for importing **demystifying**, then I moved to the folder **bpj_paper_input** and tried the command: `python run_benchmarks.py --extractor_type PCA` this...

plot_2D_potential missing

1

Hi, I am running your tutorials, thanks for releasing your instructive code on Github. In the Mueller-Brown-Potential notebook the plot_2D_potetial method seems to be missing. Is there any address where...

missing argument in bb_segsort_run

1

Hi, I am trying to build this software with GPU support: make gpu_release But I am getting these errors: nvcc -arch=native -lineinfo --expt-relaxed-constexpr --extended-lambda -DGPU_MODE -std=c++14 -Xcompiler="-Wall -Wextra" -O3 -c...