Michele Invernizzi

icon indicating a website link https://scholar.google.com/citations?user=fnJktPAAAAAJ icon indicating an email [email protected]

icon company @PeptoneLtd icon location Switzerland icon location Computational Scientist - Intrinsically Disordered Proteins, AI for Science

Results 4 issues of Michele Invernizzi

Small problem in visualizing doc

I noticed a weird minor bug in the sidebar of the documentation. If I build the user-doc locally it displays correctly: ![Screenshot from 2021-02-22 11-16-56](https://user-images.githubusercontent.com/14904699/108694764-c2e1ea00-74ff-11eb-9d35-6e096840717c.png) Instead on the plumed website...

Tutorials are harder to find

5 comment

There is no longer the "tutorials" entry in the index of plumed doc, and even links to individual tutorials are gone Master: ![Screenshot_2024-01-30-08-37-07-66_c0dc27f5c07cb0fb3541d6073dfd6932~2](https://github.com/plumed/plumed2/assets/14904699/3fed6fce-1557-4161-988a-fcf70b6ae87c) v2.9: ![Screenshot_2024-01-30-08-38-04-36_c0dc27f5c07cb0fb3541d6073dfd6932~2](https://github.com/plumed/plumed2/assets/14904699/8f4120f2-1cd2-4018-8cb1-8a94d55ac210)

Silently changing JAX default config

10 comment

I run into an error while trying to load a JAX NN model, and it took me a while to realize the problem was caused by `import pymbar`. [Here](https://github.com/choderalab/pymbar/blob/master/pymbar/mbar_solvers.py#L18) JAX...

bug
pymbar 4

adding ENERGY colvar

5 comment

Hi, is it possible to have the [ENERGY](https://www.plumed.org/doc-master/user-doc/html/_e_n_e_r_g_y.html) collective variable implemented, so that it can be biased with plumed? I would love to be able to run multithermal simulations with...