openmm / openmm-cookbook Goto Github PK

The CI has started failing for all cases. My guess is this is caused by an update in one of the upstream packages (maybe pytest itself?):

Run pytest -v --nbval-lax notebooks/cookbook
Traceback (most recent call last):
  File "/usr/share/miniconda3/envs/test/bin/pytest", line 6, in <module>
    from pytest import console_main
  File "/usr/share/miniconda3/envs/test/lib/python3.7/site-packages/pytest/__init__.py", line 5, in <module>
    from _pytest._code import ExceptionInfo
  File "/usr/share/miniconda3/envs/test/lib/python3.7/site-packages/_pytest/_code/__init__.py", line 2, in <module>
    from .code import Code
  File "/usr/share/miniconda3/envs/test/lib/python3.7/site-packages/_pytest/_code/code.py", line 35, in <module>
    import pluggy
  File "/usr/share/miniconda3/envs/test/lib/python3.7/site-packages/pluggy/__init__.py", line 16, in <module>
    from ._manager import PluginManager, PluginValidationError
  File "/usr/share/miniconda3/envs/test/lib/python3.7/site-packages/pluggy/_manager.py", line 12, in <module>
    import importlib_metadata
  File "/usr/share/miniconda3/envs/test/lib/python3.7/site-packages/importlib_metadata/__init__.py", line 6, in <module>
    import zipp
  File "/usr/share/miniconda3/envs/test/lib/python3.7/site-packages/zipp/__init__.py", line [10](https://github.com/openmm/openmm-cookbook/actions/runs/5514667050/jobs/10054182725#step:5:11), in <module>
    from .py310compat import text_encoding
  File "/usr/share/miniconda3/envs/test/lib/python3.7/site-packages/zipp/py310compat.py", line 5
    def _text_encoding(encoding, stacklevel=2, /):
                                               ^
SyntaxError: invalid syntax
Error: Process completed with exit code 1.

The notebook reads...

restraint.addGlobalParameter('k', 100.0*kilojoules_per_mole/nanometer)

should that be nm**2 instead? Thanks.

I have been learning how to use OpenMM for alchemical free energy calculations, and the tutorial notebook here has been really useful. I refer back to it frequently for reference as I apply it to a much larger system. I was able to apply all but the last cell of code, which I'm slowly working to understand. As far as I can recall, it was only a few weeks ago that the notebook worked without any issues, but as I try to run through it now, I consistently get this error:

"OpenMMException: All nonbonded Forces must agree on whether to apply a cutoff."
The error comes when I run this line: simulation = Simulation(topology, system, integrator)

I have tried exploring and investigating the error, but I haven't found any solutions. Might there be a backward compatibility issue with a new update to one of the packages downloaded?

This suggestion is from twitter:

Could this be a useful starting point for an addition to the Cookbook? It is a way to parametrize non-standard residues using a combination of openmmforcefields and ForceField. It relates to this issue and other similar requests.

TODO:

• Provide an example where energy component of a system is broken down and analyzed.

This suggestion comes from twitter:

Currently when a PR is made a gh-actions workflow tries to build and deploy the PR onto the gh-pages branch so it can be viewed. However, this only works correctly if the PR is made from a branch within the openmm/openmm-cookbook repo. It does not work from any personal forks of the cookbook. This is a github permissions issue which I do not think can be worked around.

As personal forks and PRing is the typical contribution method this gh-actions workflow becomes rather pointless and confusing by throwing workflow errors whenever someone makes a PR.

We could remove it. Or maybe make it only run if the PR comes from within the repo?

We are looking for a tool to adjust side-chain collisions, without changing the position of main-chain atoms. This is needed to elaborate transition states among different conformations, therefore they need not to respect the Rotamer Tables.
Hope you can help.
Thanks

Hi, I have been using successfully the code in the REST tutorial, many thanks for that, but I am having a most likely trivial problem. I'd like to write a trajectory file of the thermodynamic state configurations for analysis, but I just couldn't figure out how to do this. Can you show me an example? Thank you very much, Istvan

Hi,

Can rest.py run on multiple GPUs?

Thanks,

Istvan

Hello, hoping that it's not too late. I would like to suggest two tasks:

-Setting up implicit solvent calculations with newer forcefields (i.e., ff14SB)

• How to setup a replica exchange protocol in OpenMM

I would like to take a moment to thank the team of OpenMM devs, you guys keep up the great work!

Regards

The Colab notebooks are broken untilll this issue in condacolab is fixed: conda-incubator/condacolab#60

Error you get when running in colab is:

No package can be installed for pin: cudatoolkit 12.2.*

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/usr/local/lib/python3.10/site-packages/conda/exceptions.py", line 1124, in __call__
        return func(*args, **kwargs)
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 941, in exception_converter
        raise e
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 934, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 892, in _wrapped_main
        result = do_call(parsed_args, p)
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 754, in do_call
        exit_code = install(args, parser, "install")
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 547, in install
        solver.add_pin(final_spec)
    RuntimeError: No package can be installed for pin: cudatoolkit 12.2.*

`$ /usr/local/bin/mamba install openmm`

@sef43 @peastman @raimis : Here's my proposal for next steps with the openmm-cookbooks repo:

• Change the colab link to be URL-aware: Currently, the google colab link that is generated is hard-wired to the gh-pages/dev path. Instead, we want this to automatically select the path being built [dev, PR#, latest].
• Cut a major release to deploy current working state: The release action should deploy a copy of the current working state to https://openmm.github.io/openmm-cookbook/latest, allowing us to continue development work at the current URL [https://openmm.github.io/openmm-cookbook/dev]. The OpenMM webpage currently points to https://openmm.github.io/openmm-cookbook, which redirects to dev/index.html.
• Update the index.html to redirect to latest: We will want to update the gh-pages branch index.html to redirect to latest instead of dev
• Clean up the tutorials one by one: I can help clean up and add back the tutorials one by one, facilitated by being able to test them in the PR# and dev URL paths while the latest remains stable.
• Cut a new release with working tutorials
• Update openmm.org link to tutorials: We can change the openmm.org tutorials link to link out to to https://openmm.github.io/openmm-cookbook/latest/index.html#tutorials

@sef43 : Would you be able to help with the first few steps? I can then work on updating and integrating the tutorials.

We should add cookboook examples that use OpenMM-ML, OpenMM-torch, and NNPOps.

A potential problem with this is that adding PyTorch to the conda environment will make the Colab setup very slow and very brittle.

I am opening this thread to coordinate contributions to new tutorials for use in the OpenMM 8 paper.

I'll keep this list updated with the discussion below:

• Extend openmm-cookbook to build both tutorials and cookbook recipes (@ijpulidos)
• Add tutorial on computing energy components (@yuanqing-wang) #11
• Add tutorial on setting up a protein:ligand simulation from ML/MM simulations with OpenFF and AMBER force fields (@dominicrufa)

There have been 3 new additions since the last release of the cookbook:
bugfix in Alchemical free energy tutorial: #30
New CG polymer tutorial: #31
new cookbook example: #34