jhenin · jhenin · Jun 16, 2023 · May 25, 2023 · May 25, 2023 · May 30, 2023
diff --git a/SAFEP_Tutorial_Notebook.ipynb b/SAFEP_Tutorial_Notebook.ipynb
@@ -496,6 +496,14 @@
    "metadata": {},
    "outputs": [],
    "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4fb8f86f-4f20-4511-98ca-bef81bbf97fe",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/common/TI.tcl b/common/TI.tcl
@@ -45,6 +45,7 @@ proc makeTI { cvName biasType forceConst0 forceConst1 forceExp upperWalls nWindo
 	targetEquilSteps      $equilSteps     \n \
     	lambdaSchedule        $lambdaSched      \n \
 	targetNumSteps        $stepsPerWindow  \n \
+	outputEnergies	      on
         }"
 
     return $TIbias

diff --git a/stepA_create_DBC/sample_outputs/DBC_restraint.colvars b/stepA_create_DBC/sample_outputs/DBC_restraint.colvars
@@ -19,8 +19,8 @@ colvar {
         atomPermutation 1 5 3 9 7 11 12
         atoms {
             # Define ligand atoms used for RMSD calculation
-            # "auto-updating" keyword updates atom IDs when applying cfg or changing molecule
-            # auto-updating selection: "resname PHEN and noh"
+            ## "auto-updating" keyword updates atom IDs when applying cfg or changing molecule
+            ## auto-updating selection: "resname PHEN and noh"
             atomNumbers 1 3 5 7 9 11 12
 
             # Moving frame of reference is defined below
@@ -30,8 +30,8 @@ colvar {
             # if you get an error, rename this param to "rotateToReference"
             fittingGroup {
                 # Define binding site atoms used for fitting
-                # "auto-updating" keyword updates atom IDs when applying cfg or changing molecule
-                # auto-updating selection: "alpha and within 6 of resname PHEN and noh"
+                ## "auto-updating" keyword updates atom IDs when applying cfg or changing molecule
+                ## auto-updating selection: "alpha and within 6 of resname PHEN and noh"
                 atomNumbers 1207 1315 1370 1386 1556 1566 1599 1616 1730 1827
             }
             # Reference coordinates for binding site atoms

diff --git a/stepB_alchemy_site/sample_outputs/bound_convergence.pdf b/stepB_alchemy_site/sample_outputs/bound_convergence.pdf
diff --git a/stepB_alchemy_site/sample_outputs/bound_generalFigures.pdf b/stepB_alchemy_site/sample_outputs/bound_generalFigures.pdf
diff --git a/stepC_restraint_perturbation/sample_outputs/TI_general.pdf b/stepC_restraint_perturbation/sample_outputs/TI_general.pdf
diff --git a/stepD_alchemy_bulk/sample_outputs/bulk_convergence.pdf b/stepD_alchemy_bulk/sample_outputs/bulk_convergence.pdf
diff --git a/stepD_alchemy_bulk/sample_outputs/bulk_generalFigures.pdf b/stepD_alchemy_bulk/sample_outputs/bulk_generalFigures.pdf
diff --git a/text_src/Figures/COM_restraint.png b/text_src/Figures/COM_restraint.png
diff --git a/text_src/Figures/CV_COM_mismatchedRefs.png b/text_src/Figures/CV_COM_mismatchedRefs.png
diff --git a/text_src/Figures/CV_dashboard_StepA.png b/text_src/Figures/CV_dashboard_StepA.png
diff --git a/text_src/Figures/CV_dashboard_StepA_screenshot.png b/text_src/Figures/CV_dashboard_StepA_screenshot.png
diff --git a/text_src/Figures/RFEP.png b/text_src/Figures/RFEP.png
diff --git a/text_src/Figures/SAFEP_cycle.pdf b/text_src/Figures/SAFEP_cycle.pdf
diff --git a/text_src/Figures/SAFEP_cycle_old.pdf b/text_src/Figures/SAFEP_cycle_old.pdf
diff --git a/text_src/Figures/Source_images/SAFEP Cover Art.key b/text_src/Figures/Source_images/SAFEP Cover Art.key
diff --git a/text_src/Figures/Source_images/SAFEP_cycle.key b/text_src/Figures/Source_images/SAFEP_cycle.key
diff --git a/text_src/Figures/Source_images/SAFEP_cycle_old.key b/text_src/Figures/Source_images/SAFEP_cycle_old.key
diff --git a/text_src/Figures/bimodal_distribution.png b/text_src/Figures/bimodal_distribution.png
diff --git a/text_src/Figures/bound_convergence.pdf b/text_src/Figures/bound_convergence.pdf