Add Summaries for ABFE workflow

summaries/2026_jun_08_abfe/README.md

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+# Summary 2026 Jun 08 Abfe
+- Number of Datasets: 64
+- Number of Ligands: 1009
+- Total Wallclock Time: 479.57 Hours
+- Average Time Per Mol: 0.48 Hours
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+
+
+## Description
+Initial experimental ABFE workflow benchmarks.
+
+
+![Retrospective dG performance](dg_plot.png)

summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/README.md

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+# Brd4
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 25.53
+- RMSE: 25.62
+- R²: 0.74
+- Kendall 𝜏: 1.00
+- Spearman ρ: 1.00
+
+## System Details
+- Ligands: 3
+- Host Atoms: 2055
+
+## Simulation Details
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+- GPU: RTX 4090
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 1.21 Hours
+- Average Time Per Molecule: 0.40 Hours
+- Total Nanoseconds Simulated: 534.00
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 608
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_jun_08_abfe/bayer_macrocycles/brd4/dg_results.csv

@@ -0,0 +1,4 @@
+mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+61a,47.133297406893405,0.08118288902088129,13.89247731831242,0.07759108444327037,-7.3099318,-40.55075,0.11229887735351338,-12.0
+25e,40.59795440276401,0.08328969751498352,12.771085695082354,0.07998658165716004,-7.295111,-35.121983,0.11547738721210739,-11.3
+11,26.98212087280796,0.06867945587549777,2.3253710642398864,0.0681932167612316,-7.7607136,-32.41746,0.0967842056928648,-8.2

summaries/2026_jun_08_abfe/bayer_macrocycles/ftase/dg_results.csv

@@ -0,0 +1,2 @@
+mol,solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol)
+"lig 2, deprot",8.533702028703582,0.07501604126636303

summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/README.md

@@ -0,0 +1,33 @@
+# Cdk2
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 18.55
+- RMSE: 18.61
+- R²: 1.00
+- Kendall 𝜏: 1.00
+- Spearman ρ: 1.00
+
+## System Details
+- Ligands: 3
+- Host Atoms: 9185
+
+## Simulation Details
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+- GPU: RTX 4090
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 2.33 Hours
+- Average Time Per Molecule: 0.78 Hours
+- Total Nanoseconds Simulated: 550.80
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 608
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_jun_08_abfe/charge_annihilation_set/cdk2/dg_results.csv

@@ -0,0 +1,4 @@
+mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+39charg,90.22546877363595,0.08257582965752981,72.7985889657264,0.08060142733212708,-7.270515,-24.697393,0.1153921909472454,-8.37
+34,40.120661432573996,0.08163805516291812,17.90254854111144,0.076070956990173,-7.3340454,-29.55216,0.11158656974826502,-9.88
+25,37.35436788025175,0.08117936328891588,15.071258833825516,0.07391397208483001,-7.18808,-29.471188,0.10978781486736501,-9.83

summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/README.md

@@ -0,0 +1,33 @@
+# Dlk
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 23.99
+- RMSE: 24.09
+- R²: 0.17
+- Kendall 𝜏: 0.20
+- Spearman ρ: 0.50
+
+## System Details
+- Ligands: 5
+- Host Atoms: 4533
+
+## Simulation Details
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+- GPU: RTX 4090
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 2.25 Hours
+- Average Time Per Molecule: 0.45 Hours
+- Total Nanoseconds Simulated: 896.00
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 608
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_jun_08_abfe/charge_annihilation_set/dlk/dg_results.csv

@@ -0,0 +1,6 @@
+mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+9,35.026483491975654,0.08593518280354508,8.037300899162101,0.07478079102561291,-6.972359,-33.96154,0.1139167342838404,-8.73
+17charg,52.98690536047751,0.08068433816806259,23.511266326311166,0.07788800264088488,-7.150694,-36.62633,0.11214501050427866,-10.44
+4charg,55.71822585363572,0.07995489354658021,30.523484306598295,0.07397497080389523,-6.89343,-32.08817,0.10892695399891675,-9.33
+18,28.242948966055273,0.07678819292738583,4.97515736501246,0.0711212548048987,-6.8783946,-30.146185,0.10466450906623864,-9.98
+8,58.96867681546791,0.0778353080903196,29.81757616258509,0.07657409130421887,-6.9475603,-36.098663,0.10918757550464163,-10.51

summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/README.md

@@ -0,0 +1,33 @@
+# Egfr
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 41.00
+- RMSE: 41.42
+- R²: 0.27
+- Kendall 𝜏: -0.20
+- Spearman ρ: -0.50
+
+## System Details
+- Ligands: 5
+- Host Atoms: 4370
+
+## Simulation Details
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+- GPU: RTX 4090
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 2.95 Hours
+- Average Time Per Molecule: 0.59 Hours
+- Total Nanoseconds Simulated: 1034.00
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 608
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_jun_08_abfe/charge_annihilation_set/egfr/dg_results.csv

@@ -0,0 +1,6 @@
+mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+21,57.400029051999944,0.09132418607457905,12.931671895848307,0.08291253968333541,-7.8553395,-52.3237,0.12334746125853181,-9.88
+27chargR,74.80616070688536,0.09333836759198591,26.55747864714727,0.08460785441844565,-7.6062083,-55.854893,0.12597833104954828,-9.94
+28charg,63.60238286762049,0.09101379712983966,28.105795184510207,0.08623956590877757,-6.9341555,-42.430744,0.1253825107266799,-10.7
+29charg,73.96797510438594,0.0908750798899253,23.116007623435074,0.08561037278727247,-7.4772835,-58.329247,0.12484957378291714,-10.46
+30charg,72.92636113291925,0.08855975079784091,32.22275115825482,0.08383245754314463,-7.5865097,-48.29012,0.12194552225932215,-11.25

summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/README.md

@@ -0,0 +1,33 @@
+# Ephx2
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 26.29
+- RMSE: 26.98
+- R²: 0.53
+- Kendall 𝜏: 0.33
+- Spearman ρ: 0.40
+
+## System Details
+- Ligands: 4
+- Host Atoms: 5004
+
+## Simulation Details
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+- GPU: RTX 4090
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 1.78 Hours
+- Average Time Per Molecule: 0.45 Hours
+- Total Nanoseconds Simulated: 722.40
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 608
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_jun_08_abfe/charge_annihilation_set/ephx2/dg_results.csv

@@ -0,0 +1,5 @@
+mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+47charg,98.70007055354246,0.08683092418291108,67.60929140004637,0.08021258031002756,-7.792158,-38.88293,0.11821026788926195,-11.25
+19charg,83.22333632601699,0.08082503565845169,66.79436640823026,0.07491627141433276,-7.8680663,-24.297039,0.11020496409788424,-8.24
+20,44.78692274491288,0.0756835330064449,11.781804223041359,0.06958230898597266,-7.4026423,-40.40776,0.10280902145316337,-9.14
+33,41.90383152725358,0.07978697310188886,8.15782367321106,0.07273924290517396,-7.208311,-40.95432,0.1079673957043488,-10.74

summaries/2026_jun_08_abfe/charge_annihilation_set/itk/README.md

@@ -0,0 +1,33 @@
+# Itk
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 27.26
+- RMSE: 27.32
+- R²: 0.12
+- Kendall 𝜏: -0.67
+- Spearman ρ: -0.80
+
+## System Details
+- Ligands: 4
+- Host Atoms: 4776
+
+## Simulation Details
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+- GPU: RTX 4090
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 2.32 Hours
+- Average Time Per Molecule: 0.58 Hours
+- Total Nanoseconds Simulated: 774.40
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 608
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_jun_08_abfe/charge_annihilation_set/itk/dg_results.csv

@@ -0,0 +1,5 @@
+mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+17,47.190611963937435,0.0824590236592623,14.159034333927753,0.08007559183959109,-6.93884,-39.97042,0.11494168517687378,-11.27
+1charg,50.912408499563945,0.08295323355944069,15.894317650916204,0.07852629743075348,-6.9213767,-41.93947,0.11422617189659416,-12.57
+18,45.46220681023861,0.08469769907591107,13.241195453954333,0.07960645511925729,-6.9375086,-39.158516,0.11623634511377202,-12.77
+19,45.294751493131585,0.08470954376613792,14.58804697040108,0.07902528875453034,-6.9255776,-37.632282,0.11584775814751071,-13.07

summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/README.md

@@ -0,0 +1,33 @@
+# Jak1
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 22.92
+- RMSE: 23.08
+- R²: 0.06
+- Kendall 𝜏: -0.47
+- Spearman ρ: -0.66
+
+## System Details
+- Ligands: 6
+- Host Atoms: 5100
+
+## Simulation Details
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+- GPU: RTX 4090
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 2.84 Hours
+- Average Time Per Molecule: 0.47 Hours
+- Total Nanoseconds Simulated: 1027.60
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 608
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_jun_08_abfe/charge_annihilation_set/jak1/dg_results.csv

@@ -0,0 +1,7 @@
+mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+17,37.010694505291646,0.07196406120222455,10.389070631019946,0.06628909785740457,-7.2666197,-33.888245,0.0978420696810226,-10.87
+18charg,65.00809318123508,0.08058107553062685,33.98920029375755,0.07440793936518929,-7.386954,-38.405846,0.10968067821747947,-11.3
+jmc_25,31.77132570974772,0.079452121417108,8.382902989300252,0.07238645892984602,-7.3067875,-30.69521,0.10748227311552895,-11.41
+jmc_34,35.79026741372582,0.08320798926447061,9.492117602481525,0.0728836575156549,-7.19204,-33.49019,0.1106146328940956,-13.07
+16charg,67.21216301363843,0.07473884974251271,38.748290906807696,0.0726998237272144,-7.249262,-35.713135,0.10426485520443568,-10.54
+jmc_22,39.11280926200088,0.07901860535106717,12.48755331236636,0.07068068225270892,-7.2712975,-33.896553,0.10601744590083323,-11.35

summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/README.md

@@ -0,0 +1,33 @@
+# Jnk1
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 21.17
+- RMSE: 21.34
+- R²: 0.01
+- Kendall 𝜏: -0.33
+- Spearman ρ: -0.50
+
+## System Details
+- Ligands: 3
+- Host Atoms: 5993
+
+## Simulation Details
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+- GPU: RTX 4090
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 1.36 Hours
+- Average Time Per Molecule: 0.45 Hours
+- Total Nanoseconds Simulated: 496.00
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 608
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_jun_08_abfe/charge_annihilation_set/jnk1/dg_results.csv

@@ -0,0 +1,4 @@
+mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+6a,35.05677176705646,0.06818299316838441,12.323812260514739,0.06624380490768736,-7.4312205,-30.164179,0.09506399026996341,-8.41
+19b_charg,92.76071946815068,0.07721219722133342,75.22082016432068,0.07331111024121917,-7.3782635,-24.918163,0.10647179102723069,-7.3
+19a_charg,49.248852545944395,0.07300066516742226,25.56239904327995,0.07147454412842849,-7.318644,-31.005096,0.10216509958519479,-6.86

summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/README.md

@@ -0,0 +1,33 @@
+# Ptp1B
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 29.10
+- RMSE: 29.55
+- R²: 0.52
+- Kendall 𝜏: 0.33
+- Spearman ρ: 0.50
+
+## System Details
+- Ligands: 3
+- Host Atoms: 5163
+
+## Simulation Details
+- TMD Sha: [e393f948bec757f86ae1d25908107665ac16b907](https://github.com/tmd-industries/tmd/tree/e393f948bec757f86ae1d25908107665ac16b907)
+- GPU: RTX 4090
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 1.79 Hours
+- Average Time Per Molecule: 0.60 Hours
+- Total Nanoseconds Simulated: 656.80
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 608
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_jun_08_abfe/charge_annihilation_set/ptp1b/dg_results.csv

@@ -0,0 +1,4 @@
+mol,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),complex correction (kcal/mol),pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+26charg,102.1946467041906,0.08576447016244779,72.71683462498555,0.07995209903654799,-7.148156,-36.625973,0.11725136452338358,-7.44
+27,171.313708477713,0.09583506472463406,146.81549570771816,0.08751470413881678,-7.4514866,-31.949686,0.12978128937285002,-9.23
+32,190.0950039528491,0.11207762077789028,149.96070686682273,0.08990471319833117,-6.7815003,-46.915787,0.1436810722903569,-11.53