Add basic example with sample files #58
Conversation
|
I'm not sure what's going on. I just told it to rerun all checks, but I'm not convinced it's really doing anything. |
|
Looks it it never really ran the checks either again? |
|
Any updates/luck with running these checks? |
|
Updated this PR into the latest commit in @peastman let me know if you have any other feedback on this PR! The checks appear to be at the "Expected" stage for some reason. |
|
Sorry, but I still could not find such an example script. |
|
I imagine this PR needs to be merged for the example scripts to be added into the main branch. If you're looking for the example scripts I wrote in this PR you could probably find them fastest in the "files changed" tab? Separately, it does look like all the checks still never ran again, and still need to be rerun prior to merging? |
|
Sorry, it's my fault for having dropped this. I'm not sure what went wrong with the checks, and since then CI got disabled due to lack of activity. Anyway, I've reenabled it. Let's see if we can get this merged. A couple of minor suggestions. I don't think this line is ever used for anything: molecule = Modeller(pdb.topology,pdb.positions)I also suggest removing this: # define the platform as OpenCL by default (since CUDA may not always exist)
platform = openmm.Platform.getPlatformByName('OpenCL')Just let the simulation pick the fastest platform automatically. Otherwise people will copy your code and use OpenCL when they really should use something else! Sorry again for forgetting this. |
|
No worries at all! Everything is Chaos now anyways. I've made the following changes and pushed them in the latest commit:
It should be good to rerun the workflow checks again now, if you get a chance! |
|
Thanks! CI is failing, but it's not related to this. I'll fix it in a separate PR. |
Address #49 : Providing a basic example script for running the plumed-openmm plugin in a basic metadynamics simulation.
The script
examples/basic-example/plumed-metad-sim.pyis a single script contains reads in a system, state, and topology and runs a metadynamics simulation using the PLUMED scripting language to define collective variables. A sample output file from PLUMED,colvar, is also included.The subdirectory
basic-examplewas created to prevent future confusion if other more advanced examples get added.