OpenFreeEnergy · jthorton · Sep 5, 2025 · Sep 22, 2025 · Oct 8, 2025 · Oct 8, 2025
diff --git a/environment.yaml b/environment.yaml
@@ -16,3 +16,5 @@ dependencies:
   - python
   - openfe==1.11.0
   - openff-interchange-base != 0.5.1  # https://github.com/openforcefield/openff-interchange/issues/1450
+  - pip:
+    - git+https://github.com/OpenFreeEnergy/openfe_analysis@main
diff --git a/simulation_visualisation/images/centered_system.png b/simulation_visualisation/images/centered_system.png
diff --git a/simulation_visualisation/images/hybrid_system.png b/simulation_visualisation/images/hybrid_system.png
diff --git a/simulation_visualisation/images/hybrid_system_state_1.png b/simulation_visualisation/images/hybrid_system_state_1.png
diff --git a/simulation_visualisation/images/septop_full.png b/simulation_visualisation/images/septop_full.png
diff --git a/simulation_visualisation/images/septop_state_a.png b/simulation_visualisation/images/septop_state_a.png
diff --git a/simulation_visualisation/images/statea_ligand.png b/simulation_visualisation/images/statea_ligand.png
diff --git a/simulation_visualisation/simulation_visualisation.ipynb b/simulation_visualisation/simulation_visualisation.ipynb
diff --git a/simulation_visualisation/topologies/alchemical_system_septop.pdb b/simulation_visualisation/topologies/alchemical_system_septop.pdb
@@ -0,0 +1,62 @@
+ATOM      1  C1x UNK A   1      25.978   5.327   4.779  1.00  0.00           C  
+ATOM      2  C2x UNK A   1      26.395   5.074   3.499  1.00  0.00           C  
+ATOM      3  C3x UNK A   1      27.340   5.860   2.902  1.00  0.00           C  
+ATOM      4  C4x UNK A   1      27.837   6.921   3.569  1.00  0.00           C  
+ATOM      5  C5x UNK A   1      27.420   7.196   4.856  1.00  0.00           C  
+ATOM      6  C6x UNK A   1      26.498   6.379   5.469  1.00  0.00           C  
+ATOM      7  H1x UNK A   1      25.230   4.686   5.245  1.00  0.00           H  
+ATOM      8  H2x UNK A   1      25.968   4.235   2.950  1.00  0.00           H  
+ATOM      9  H3x UNK A   1      27.689   5.631   1.895  1.00  0.00           H  
+ATOM     10  H4x UNK A   1      28.573   7.566   3.089  1.00  0.00           H  
+ATOM     11  H5x UNK A   1      27.821   8.060   5.386  1.00  0.00           H  
+ATOM     12  H6x UNK A   1      26.187   6.572   6.496  1.00  0.00           H  
+TER      13      UNK A   1
+ATOM     14  H1x UNK B   1      37.049   8.204   4.787  1.00  0.00           H  
+ATOM     15  H2x UNK B   1      36.339   7.604   6.304  1.00  0.00           H  
+ATOM     16  C1x UNK B   1      36.128   7.877   5.270  1.00  0.00           C  
+ATOM     17  H3x UNK B   1      35.400   8.687   5.248  1.00  0.00           H  
+ATOM     18  C2x UNK B   1      34.120   4.787   4.444  1.00  0.00           C  
+ATOM     19  C3x UNK B   1      34.537   4.534   3.164  1.00  0.00           C  
+ATOM     20  C4x UNK B   1      35.482   5.320   2.567  1.00  0.00           C  
+ATOM     21  C5x UNK B   1      35.979   6.381   3.234  1.00  0.00           C  
+ATOM     22  C6x UNK B   1      35.562   6.656   4.521  1.00  0.00           C  
+ATOM     23  C7x UNK B   1      34.640   5.839   5.134  1.00  0.00           C  
+ATOM     24  H4x UNK B   1      33.372   4.146   4.910  1.00  0.00           H  
+ATOM     25  H5x UNK B   1      34.110   3.696   2.614  1.00  0.00           H  
+ATOM     26  H6x UNK B   1      35.831   5.092   1.560  1.00  0.00           H  
+ATOM     27  H7x UNK B   1      36.715   7.026   2.754  1.00  0.00           H  
+ATOM     28  H8x UNK B   1      34.329   6.032   6.160  1.00  0.00           H  
+TER      29      UNK B   1
+ATOM     30 Na    NA D   1      17.857  -4.057  -2.352  1.00  0.00          Na  
+ATOM     31 Na    NA D   2      41.388   6.331  12.660  1.00  0.00          Na  
+ATOM     32 Cl    CL D   3      37.257  -6.694  -1.840  1.00  0.00          Cl  
+ATOM     33 Cl    CL D   4      30.875  -3.775   0.157  1.00  0.00          Cl  
+TER      34       CL D   4
+CONECT    1    2    6    7
+CONECT    2    1    3    8
+CONECT    3    2    4    9
+CONECT    4    3    5   10
+CONECT    5    4    6   11
+CONECT    6    1    5   12
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+CONECT   14   16
+CONECT   15   16
+CONECT   16   14   15   17   22
+CONECT   17   16
+CONECT   18   19   23   24
+CONECT   19   18   20   25
+CONECT   20   19   21   26
+CONECT   21   20   22   27
+CONECT   22   16   21   23
+CONECT   23   18   22   28
+CONECT   24   18
+CONECT   25   19
+CONECT   26   20
+CONECT   27   21
+CONECT   28   23
+END