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REMD Workflow Automation #36

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REMD Workflow Automation #36

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b13ac1e
added basic tests for gromacs wrapper and topology builder
Feb 29, 2024
bf046c6
added conda-forge gromacs for simple wrapper tests
Feb 29, 2024
4eaa011
have a working gmx wrapper that can run minimizations on single folda…
Mar 1, 2024
38ecae7
adding workflow functions to parameterize entire box
Mar 2, 2024
4001757
made TopologyGenerator a bit more general, so it can handle both sing…
Mar 2, 2024
676b0dd
added a doc keyword for system and foldamer file prefixes to not have…
Mar 2, 2024
c68f92a
added some logic to give the option of a file prefix in the system bu…
Mar 5, 2024
3ca25c5
separated single molecule topology generation and system topology gen…
Mar 6, 2024
3ee8bbb
changed tests to reflect most recent changes to the system builders/t…
Mar 12, 2024
75ff323
added a topology manager object which stores topologies locally after…
May 10, 2024
c5d4d86
added functionality to add structures to local databased of structure…
Aug 6, 2024
9825932
added topology library to repository with some initial molecule files
Aug 23, 2024
8164900
added topology to topology builders
Aug 29, 2024
6d7b94e
foldamer parameterization is now aware of the topology manager. Next …
Sep 6, 2024
48a3cd3
implemented openff workflow for building and parameterizing system, a…
Sep 6, 2024
e7f016a
fixed test_topology_generator test and made it so that topology_manag…
Sep 6, 2024
02c7b32
removed asserts to of loading top_manager from file, in a clean insta…
Sep 6, 2024
cecdd6e
removed absolute path of top files so that they can be accessed on an…
Sep 10, 2024
704a72d
working bespoke flow parameterization with xtc, need to see if I can …
Sep 17, 2024
9a9029a
updated submission scripts for ascent allocation, and changed submiss…
Sep 17, 2024
c925c72
updated topology manager and simulation filesystem
Sep 17, 2024
11f13f0
Merge branch 'workflow_parameterization' of https://github.com/shirts…
Sep 17, 2024
9dd7323
updated test_env to include bespokefit and other requirements
Sep 17, 2024
f9e2589
Merge branch 'workflow_parameterization' of https://github.com/shirts…
Sep 17, 2024
a4542f8
updated topology_manager
Sep 17, 2024
cfab4bd
added openeye to environment file
Sep 18, 2024
4a51137
merged with remote
Sep 18, 2024
4eacf38
started generating parameters for other terphenyl chemistry
Sep 24, 2024
c79a43f
rebuilding topology manager files
Sep 24, 2024
3c176d2
starting to update build files to have the correct smiles string for …
Sep 24, 2024
e556483
reran some parameterization on my laptop
Sep 26, 2024
1b05032
added pmp and mom parameters, fixed bespoke parameter assignment to w…
Sep 26, 2024
e5bd495
Merge branch 'workflow_parameterization' of https://github.com/shirts…
Sep 26, 2024
ff676ec
merged with remote
Sep 26, 2024
6715cb2
added mop_bespoke tetramer topology
Sep 27, 2024
57c2358
added ff storage in topology manager for offxml files
Sep 27, 2024
15a5a18
added logic to topology manager to use bepsoke FF if it is available …
Sep 27, 2024
bd5b9a6
working simulations on alpine, added some generated topologies
Sep 27, 2024
458aeb8
merged with remote
Sep 27, 2024
a596f9f
fixed topology_manager after merge
Sep 27, 2024
f7896fe
added bespoke ff for mom and pom foldamers
Oct 1, 2024
30a4f69
merged with remote
Oct 1, 2024
28f0a42
added pop bespoke FF
Oct 7, 2024
1360550
added default openff parameters to topologymanager for all terphenyl …
Oct 7, 2024
741813e
updated topology_manager tests to account for removed print statement…
Oct 7, 2024
9738d34
removed 3.9 from testing since I use some function() -> None: formati…
Oct 7, 2024
eee5bd3
merged with remote
Oct 7, 2024
421d185
started updating analysis workflow into new remd workflow file
Nov 3, 2024
7053e3f
Merge branch 'workflow_parameterization' of https://github.com/shirts…
Nov 3, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/python-package.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12"]
python-version: ["3.10", "3.11", "3.12"]

steps:
- uses: actions/checkout@v4
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33 changes: 22 additions & 11 deletions environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,29 +2,40 @@ name: terphenyl
channels:
- conda-forge
- omnia
- openeye
dependencies:
- python
- pip
- python=3.11
- ca-certificates
- openssl
- ambertools
- openeye-toolkits
- psi4
- dftd3-python
- xtb-python
- mbuild
- tqdm
- pytest
- rdkit
- pyyaml
- mbuild=0.14.2
- mdtraj
- numpy
- matplotlib
- scikit-learn
- tqdm
- mdanalysis
- signac
- signac-flow
- panedr
- pandas
- seaborn
- openff-toolkit
- mbuild ==0.14.2
- rdkit
- ca-certificates
- certifi
- openssl
- gromacs
- openbabel
prefix: /home/lenny/miniforge3/envs/terphenyl
- certifi
- openmm
- openff-units
- cachetools
- xmltodict
- openff-toolkit
- openff-bespokefit
- openff-interchange
- qcportal[version='<0.50']
prefix: /home/lenny/miniforge3/envs/ts_env
6 changes: 2 additions & 4 deletions examples/generate_bespoke_fit_parameters/mom/mom_bespoke.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -62,9 +62,7 @@
"cell_type": "code",
"execution_count": 3,
"id": "e018bd1b",
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [
{
"name": "stdout",
Expand Down Expand Up @@ -997,7 +995,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.10"
"version": "3.11.10"
}
},
"nbformat": 4,
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6 changes: 2 additions & 4 deletions examples/generate_bespoke_fit_parameters/pom/pom_bespoke.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -66,9 +66,7 @@
"cell_type": "code",
"execution_count": 3,
"id": "e018bd1b",
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [
{
"name": "stdout",
Expand Down Expand Up @@ -1374,7 +1372,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.15"
"version": "3.11.8"
}
},
"nbformat": 4,
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3 changes: 3 additions & 0 deletions simulations/.gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
*workspace
*.signac
*signac_project_document.json
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