Merge pull request #170 from ricalessandri/example-links

Small fixes of the openmm examples

Author: ricalessandri

examples/README.md

@@ -34,8 +34,11 @@ Examples for Methods using OpenMM can be found in the subfolder [openmm](openmm)
 
 ### Script examples
 
-* ABF with Alanine Dipeptide: [ABF](openmm/abf)
+* ABF with Alanine Dipeptide: [ABF](openmm/abf/alanine-dipeptide_openmm.py)
 * Forward flux sampling with Alanine Dipeptide: [FFS](openmm/forward_flux_sampling.py)
+* Metadynamics with Alanine Dipeptide: [Metadynamics](openmm/metad/alanine-dipeptide.py)
+* Spectral ABF with Alanine Dipeptide: [SpectralABF](openmm/spectral_abf/alanine-dipeptide.py)
+* Umbrella integration with Alanine Dipeptide: [Umbrella Integration](openmm/umbrella_integration/integration.py)
 
 ## Installation of the Environment
 

examples/openmm/metad/Metadynamics-ADP.ipynb

@@ -327,7 +327,7 @@
    },
    "outputs": [],
    "source": [
-    "state = pysages.run(method, generate_simulation, timesteps)"
+    "run_result = pysages.run(method, generate_simulation, timesteps)"
    ]
   },
   {

examples/openmm/metad/Metadynamics-ADP.md

@@ -199,7 +199,7 @@ On the GPU this should run in around half an hour.
 <!-- #endregion -->
 
 ```python id="K951m4BbpUar"
-state = pysages.run(method, generate_simulation, timesteps)
+run_result = pysages.run(method, generate_simulation, timesteps)
 ```
 
 <!-- #region id="PXBKUfK0p9T2" -->