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Fixes for new openmmtools 0.23.0 #1203

Merged
merged 28 commits into from
Jun 15, 2023
Merged

Fixes for new openmmtools 0.23.0 #1203

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bd4c691
change default to none
mikemhenry Apr 18, 2023
a235671
Merge branch 'main' into feat/set_default_to_none_for_atom_selection
mikemhenry Apr 25, 2023
2820950
Changing default in template yaml file
ijpulidos May 30, 2023
a71fc09
Test null/none atom selection
ijpulidos May 30, 2023
0226dd5
null atom selection should be empty list
ijpulidos May 30, 2023
bd3a6e6
Merge branch 'main' into feat/set_default_to_none_for_atom_selection
ijpulidos May 30, 2023
3de54db
Document how to control the log level in the CLI
mikemhenry May 30, 2023
26046e7
Update examples/new-cli/README.md
mikemhenry May 31, 2023
754baa1
Add solvent_model kwarg to RelativeFEPSetup
ijpulidos Jun 5, 2023
135dc60
Specify solvent model input YAML/CLI
ijpulidos Jun 5, 2023
24dfaa0
Test openmmtools_dev
mikemhenry Jun 9, 2023
41bff85
Update CI.yaml
mikemhenry Jun 9, 2023
851f822
Update CI.yaml
mikemhenry Jun 9, 2023
6364535
make sure we pull in openmmtools
mikemhenry Jun 9, 2023
65fae3b
forgot to add new env file
mikemhenry Jun 9, 2023
d061e90
Online analysis multiple of checkpoint interval. Fix tests.
ijpulidos Jun 9, 2023
0474f9a
Using dask import inside functions
ijpulidos Jun 9, 2023
1505004
Merge branch 'feat/set_default_to_none_for_atom_selection' into mikem…
ijpulidos Jun 9, 2023
1a7f712
Merge remote-tracking branch 'origin/mikemhenry-patch-2' into mikemhe…
ijpulidos Jun 9, 2023
cd0e440
Merge branch '1192-add-solvent-model-cli' into mikemhenry-patch-3
ijpulidos Jun 9, 2023
8cfbb49
dask import inside functions
ijpulidos Jun 9, 2023
2df9be9
Pinning dask version
ijpulidos Jun 9, 2023
cae139e
set CI to just pull from normal channels since we pushed update
mikemhenry Jun 12, 2023
273c880
Drop 3.8 testing
mikemhenry Jun 12, 2023
0149438
Testing with ambertools < 23
ijpulidos Jun 13, 2023
7a38a07
Revert "Merge branch '1192-add-solvent-model-cli' into mikemhenry-pat…
ijpulidos Jun 15, 2023
ca3c43e
Revert "Merge remote-tracking branch 'origin/mikemhenry-patch-2' into…
ijpulidos Jun 15, 2023
6afba88
Revert "Merge branch 'feat/set_default_to_none_for_atom_selection' in…
ijpulidos Jun 15, 2023
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Revert "Merge remote-tracking branch 'origin/mikemhenry-patch-2' into… 
… mikemhenry-patch-3"

This reverts commit 1a7f712, reversing
changes made to 1505004.
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@ijpulidos
ijpulidos committed Jun 15, 2023
commit ca3c43e6b2ac06f1332318104aed5cade32321cc
13 changes: 0 additions & 13 deletions examples/new-cli/README.md
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Expand Up @@ -45,19 +45,6 @@ Currently only `key:value` parts of the yaml can be overridden i.e. not sequence

To view all options ultimately used in the simulation, a file named `perses-$date-$yaml_name.yaml` is created under the simulation/experiment directory.

The `LOGLEVEL` environment variable is used to control the logging messages printed to the terminal.
Two common methods to set this environmental variable are:
1. Setting the environmental variable for all applications ran in the terminal session
```bash
$ export LOGLEVEL=DEBUG # This will set the log level to DEBUG for all programs ran after this export
$ perses-cli --yaml template.yaml
```
2. Setting the environmental variable for only one command
```bash
$ LOGLEVEL=DEBUG perses-cli --yaml template.yaml
```


## Example Use Case

In this example folder we have a protein: [2ZFF](https://www.rcsb.org/structure/2zff) and some ligands which we will use for a series of free energy calculations.
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