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Update the tutorial for OpenMM 8.0 #85

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17022c5
Install MambaForge explicitly
Oct 25, 2022
3fdfa9d
Use OpenMM 8.0beta and friends
Oct 25, 2022
04281cd
Remove circumvent for #61
Oct 25, 2022
11b8d1a
Clean up
Oct 25, 2022
4e67ec9
Merge branch 'master' into tut_8b
Oct 26, 2022
63ac66b
Fix typo
Oct 26, 2022
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74 changes: 28 additions & 46 deletions tutorials/openmm-torch-nnpops.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@
"base_uri": "https://localhost:8080/"
},
"id": "EcB2lc1s3ZXG",
"outputId": "1ce0bad8-a050-48d5-c18a-9e49fbeb11c2"
"outputId": "ca3b9161-9de2-4fc3-a497-235011951876"
},
"outputs": [
{
Expand All @@ -50,15 +50,15 @@
"📦 Installing...\n",
"📌 Adjusting configuration...\n",
"🩹 Patching environment...\n",
"⏲ Done in 0:00:34\n",
"⏲ Done in 0:00:18\n",
"🔁 Restarting kernel...\n"
]
}
],
"source": [
"!pip install -q condacolab\n",
"import condacolab\n",
"condacolab.install_miniconda()"
"condacolab.install_mambaforge()"
]
},
{
Expand All @@ -82,11 +82,17 @@
},
"outputs": [],
"source": [
"# NOTE: PyTorch pinned because https://github.com/conda-forge/openmm-torch-feedstock/issues/20\n",
"!mamba install -q -c conda-forge \\\n",
" openmm-torch nnpops torchani openmmtools \\\n",
" pytorch=1.11 \\\n",
" &> /dev/null # Comment this line to see a log\""
"# Note: at the moment only the beta releases work correctly.\n",
"!mamba install -q \\\n",
" -c conda-forge/label/openmm_rc \\\n",
" -c conda-forge/label/openmm-torch_rc \\\n",
" -c conda-forge \\\n",
" openmm==8.0.0beta \\\n",
" openmm-torch==1.0beta \\\n",
" nnpops==0.2 \\\n",
" torchani==2.2.2 \\\n",
" openmmtools \\\n",
" &> /dev/null # Comment this line to see a log"
Comment on lines +85 to +95
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@RaulPPelaez RaulPPelaez May 2, 2023

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This should be good to go with a some changes here, right?
I guess removing the channels and the betas should do the trick, also nnpops to 0.5?

]
},
{
Expand All @@ -110,15 +116,7 @@
"id": "zNng_d4mGKve",
"outputId": "218e0775-766b-4597-9d48-96e3d65df374"
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.\n"
]
}
],
"outputs": [],
"source": [
"import openmmtools\n",
"\n",
Expand Down Expand Up @@ -159,29 +157,13 @@
"outputId": "4181fcb6-db72-47e7-edb5-2a4bb0252de7"
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/local/lib/python3.7/site-packages/torchani/__init__.py:55: UserWarning: Dependency not satisfied, torchani.ase will not be available\n",
" warnings.warn(\"Dependency not satisfied, torchani.ase will not be available\")\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"/usr/local/lib/python3.7/site-packages/torchani/resources/\n",
"Downloading ANI model parameters ...\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/local/lib/python3.7/site-packages/torch/functional.py:1069: UserWarning: torch.meshgrid: in an upcoming release, it will be required to pass the indexing argument. (Triggered internally at /home/conda/feedstock_root/build_artifacts/pytorch-recipe_1640851336451/work/aten/src/ATen/native/TensorShape.cpp:2156.)\n",
" return _VF.cartesian_prod(tensors) # type: ignore[attr-defined]\n"
]
}
],
"source": [
Expand Down Expand Up @@ -322,7 +304,7 @@
"# Create a simulation and set the initial positions and velocities\n",
"simulation = Simulation(ala2.topology, ala2.system, integrator)\n",
"simulation.context.setPositions(ala2.positions)\n",
"# simulation.context.setVelocitiesToTemperature(temperature) # This does not work (https://github.com/openmm/openmm-torch/issues/61)\n",
"simulation.context.setVelocitiesToTemperature(temperature)\n",
"\n",
"# Configure a reporter to print to the console every 0.1 ps (100 steps)\n",
"reporter = StateDataReporter(file=sys.stdout, reportInterval=100, step=True, time=True, potentialEnergy=True, temperature=True)\n",
Expand All @@ -346,7 +328,7 @@
"base_uri": "https://localhost:8080/"
},
"id": "JN9v2rz3KbTz",
"outputId": "15367844-1caa-40c1-bb5b-f94f7b51eb1b"
"outputId": "7ef59ac1-520a-4076-a1c5-fc2ec7df5136"
},
"outputs": [
{
Expand Down Expand Up @@ -390,24 +372,24 @@
"base_uri": "https://localhost:8080/"
},
"id": "da0v6qJHBtUb",
"outputId": "e477991e-93b0-4e72-de4f-d7a8b05052de"
"outputId": "bc7426d5-42dc-455a-d20d-733e51ea644f"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"#\"Step\",\"Time (ps)\",\"Potential Energy (kJ/mole)\",\"Temperature (K)\"\n",
"100,0.10000000000000007,-1301527.998092823,62.28599411217165\n",
"200,0.20000000000000015,-1301519.2141580286,68.6151680329106\n",
"300,0.3000000000000002,-1301513.905558333,103.32518127627559\n",
"400,0.4000000000000003,-1301517.7584694924,118.20611762387\n",
"500,0.5000000000000003,-1301514.9794064017,165.4939713543869\n",
"600,0.6000000000000004,-1301507.6431399288,148.54034468306415\n",
"700,0.7000000000000005,-1301511.109281123,157.43310789810866\n",
"800,0.8000000000000006,-1301498.8263809385,157.8375886414082\n",
"900,0.9000000000000007,-1301511.3014532926,199.2036328097003\n",
"1000,1.0000000000000007,-1301485.2554342675,148.26160451888617\n"
"100,0.10000000000000007,-1301523.916390367,92.40824830382874\n",
"200,0.20000000000000015,-1301518.7990238892,119.2893445291452\n",
"300,0.3000000000000002,-1301513.695350461,152.9633322198495\n",
"400,0.4000000000000003,-1301508.793747321,161.74950978774066\n",
"500,0.5000000000000003,-1301504.6699876415,164.00853843792856\n",
"600,0.6000000000000004,-1301498.9500878605,159.56241762805863\n",
"700,0.7000000000000005,-1301508.518243164,197.16748430772566\n",
"800,0.8000000000000006,-1301501.4794679733,217.2560582437653\n",
"900,0.9000000000000007,-1301479.1362451615,189.695421119118\n",
"1000,1.0000000000000007,-1301481.766797349,256.3789993541881\n"
]
}
],
Expand Down