Update OpenMM Colab notebooks

SSAGESLabs · Oct 31, 2024 · 1e67592 · 1e67592
1 parent 2a7b5f4
commit 1e67592
Show file tree

Hide file tree

Showing 10 changed files with 183 additions and 1,154 deletions.
diff --git a/.trunk/trunk.yaml b/.trunk/trunk.yaml
@@ -41,7 +41,7 @@ lint:
       paths:
         - examples/Advanced_Sampling_Introduction.md
         - examples/Installing_a_PySAGES_Environment.md
-        - examples/openmm/Harmonic_Bias.md
+        - examples/openmm/harmonic_bias/Harmonic_Bias.md
         - examples/hoomd-blue/ann/Butane_ANN.md
         - examples/hoomd-blue/harmonic_bias/Harmonic_Bias.md
         - examples/openmm/metad/Metadynamics-ADP.md
@@ -55,7 +55,7 @@ lint:
       paths:
         - examples/Advanced_Sampling_Introduction.ipynb
         - examples/Installing_a_PySAGES_Environment.ipynb
-        - examples/openmm/Harmonic_Bias.ipynb
+        - examples/openmm/harmonic_bias/Harmonic_Bias.ipynb
         - examples/hoomd-blue/ann/Butane_ANN.ipynb
         - examples/hoomd-blue/harmonic_bias/Harmonic_Bias.ipynb
         - examples/openmm/metad/Metadynamics-ADP.ipynb

diff --git a/examples/README.md b/examples/README.md
@@ -45,7 +45,7 @@ Examples for Methods using OpenMM can be found in the subfolder [openmm](openmm)
 
 ### OpenMM notebooks
 
-- Harmonic bias for the dihedral angle of Alanine Dipeptide: [![Harmonic Bias](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/openmm/Harmonic_Bias.ipynb)
+- Harmonic bias for the dihedral angle of Alanine Dipeptide: [![Harmonic Bias](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/openmm/harmonic_bias/Harmonic_Bias.ipynb)
 - Metadynamics sampling with Alanine Dipeptide: [![Metadynamics](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/openmm/metad/Metadynamics-ADP.ipynb)
 - Metadynamics sampling with NaCL [![MetadynamicsNaCl](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/openmm/metad/nacl/Metadynamics_NaCl.ipynb)
 - Spectral ABF sampling with Alanine Dipeptide: [![SpectralABF](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/openmm/spectral_abf/ADP_SpectralABF.ipynb)