Iván Pulido

Results 170 comments of Iván Pulido

This sounds like something we definitely should improve. Thanks for the feedback! I don't know if @mikemhenry is already working on this, but I'm happy to give this a try,...

Thanks for the feedback. We would need to dig into this, but as far as I know there is no easy way to access the replica positions directly from the...

According to https://github.com/choderalab/openmmtools/runs/7661564216?check_suite_focus=true#step:7:3003 we shouldn't import `Iterable` directly from collections but we should be using `collections.abc.Iterable` instead (https://docs.python.org/3/library/collections.abc.html#collections.abc.Iterable). This should fix the tests erroring with python 3.10.

Good catch! This happens when trying to directly read the mcmc moves using the public API point `MultiStateReporter.read_mcmc_moves`. Just to realize that when resuming the simulations the moves are instantiated...

To reproduce the problem you can use the nc files attached here and run the following script using them ```python #!/bin/env python # Directly read the mcmc_moves from reporter from...

> I thought we had this tested? So, it was tested by resuming simulation, which use the `MultiStateSampler.from_storage` method, but we didn't really test using the `reporter.read_mcmc_moves` public API point...

Just made a script to show the problem also happens with rdkit, fwiw. Inspired in @SimonBoothroyd previous code. https://gist.github.com/ijpulidos/7b0b9ac7d3e4a1692a1dee2825da3b98

I see. Then I guess the issue is that if you create your environments in a node without CUDA capabilities then you can end up in this situation. This is...

In any case, I think this is not an issue with openmm, whatsoever. It is rather an issue with HPC system not having the latest drivers or conda defaulting to...

For the instructions for having [Using local build of OpenMM alongside conda tools that depend on it](https://github.com/openmm/openmm/blob/master/docs-source/usersguide/library/02_compiling.rst#using-local-build-of-openmm-alongside-conda-tools-that-depend-on-it) I think what we want to recommend is to have two separate environments,...