Eugen Hruška

icon indicating a website link https://hruska-lab.github.io

icon company Charles University icon location computational pharmaceutical science | high-throughput atomistic simulation and explainable machine learning

Results 4 issues of Eugen Hruška

Koopman ignores dim setting

6 comment

koopman ignores the number of dimensions requested, and later gives fatal error. Here koopman method of tica generates 3 dimensions, but I have set dim=5 for the tica. tica_obj calculation...

bug
coordinates

relative entropy between two MSM matrices

2 comment

feature request: calculation of the relative entropy between two MSM matrices of the same protein, like in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637129/

feature-request

minimal extxyz

The minimal example for extxyz with exact .extxyz and .yaml files as described in docs/howto/dataset.rst fails in colab: https://colab.research.google.com/drive/1GLdSM5FPOgZz3LAkkH1nIEujCf08F32z?usp=sharing Error is ''RuntimeError: Failed to build object with prefix `dataset` using...

bug

DFT energy of single atom no convergence

For enthalpy of atomization I calculate the DFT energy of single atoms, but don't reach convergence for oxygen atom: ``` > DFT BASIS=6-31+G(d) B3LYP D3 ENERGY > > O 0.000...