Reaction Field With Precomputed using rxn field

summaries/2026_apr_23/README.md

@@ -0,0 +1,14 @@
+# Summary
+- Number of Datasets: 14
+- Number of Ligands: 353
+- Number of Edges: 607
+- Total Wallclock Time: 83.73 Hours
+- Average Time Per Edge: 0.14 Hours
+- TMD Sha: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427)
+
+
+## Description
+Results of switching to Reaction Field from the custom real space PME implementation inherited from Timemachine.
+
+
+![Retrospective dG performance](dg_plot.png)

summaries/2026_apr_23/fragments/mcl1/README.md

@@ -0,0 +1,40 @@
+# Mcl1 Map
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 0.66
+- RMSE: 0.86
+- R²: 0.24
+- Kendall 𝜏: 0.18
+- Spearman ρ: 0.27
+
+## System Details
+- Ligands: 12
+- Host Atoms: 2428
+- Map Details:
+  - Edges: 20
+  - Min Dummy Atoms: 2
+  - Max Dummy Atoms: 19
+  - Mean Dummy Atoms: 7.2
+  - Median Dummy Atoms: 6.0
+
+## Simulation Details
+- TMD Sha: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427)
+- GPU: RTX 5090, RTX 50080
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 1.57 Hours
+- Average Time Per Edge: 0.08 Hours
+- Total Nanoseconds Simulated: 2216.80
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 422
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - REST: Temperature Scale 3.0
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_apr_23/fragments/mcl1/ddg_results.csv

@@ -0,0 +1,21 @@
+mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol)
+11,14,-5.529757983783047,0.0640674841211962,-5.886120930104273,0.06337169613653576,-0.0600000000000005,0.35636294632122595,0.09011445163147334,0.481658755273048,0.07164441919664735
+10,15,-1.2133157260254024,0.06568631213721997,-1.0375669641561465,0.06396081478604689,-0.2699999999999996,-0.1757487618692558,0.09168248158881437,-0.3743346744192593,0.07502569737477952
+2,13 flipped,4.278683881330554,0.05685845065956202,1.9498584538842927,0.054886256326515344,0.1200000000000001,2.3288254274462616,0.07902774541226514,2.1531820879835424,0.055541983278263714
+2,14,1.7662506510772407,0.06545701428193855,2.1853887487247055,0.06643404229715566,-0.28000000000000025,-0.4191380976474647,0.09326361935206125,-0.17889513059760453,0.05903692160779348
+2,3,0.5677836340830087,0.045142028529103526,2.7891820674362204,0.04601330353612805,-1.0599999999999996,-2.2213984333532117,0.06445949768676645,-2.15291720133583,0.057303437544123086
+2,15,14.267290294936979,0.0717930537878102,15.270569875312216,0.07102531631443867,0.020000000000000462,-1.0032795803752377,0.10098929710491837,-0.8107734038494385,0.06444898719093037
+2,4,-4.857103470836736,0.04302544236044111,-4.630854888304673,0.04278723005697917,-0.47999999999999954,-0.22624858253206365,0.06067895637089107,-0.2301226672084491,0.05241313665341936
+2,5,0.6171208246742383,0.04514345392763493,0.44214222187786517,0.04361657429816907,-0.71,0.1749786027963732,0.0627721035653912,0.041790838036591005,0.05423435828160568
+3,4,-5.70477562707599,0.05244174576223522,-7.463287803622189,0.05381100455787853,0.5800000000000001,1.7585121765461984,0.0751382785943286,1.922794534127381,0.06464267667045868
+3,11,6.64138988759355,0.06290355904536601,5.048752579711695,0.06317268146352294,0.8399999999999999,1.5926373078818545,0.08914956771552839,1.4923633154651776,0.07022284986721485
+4,11,12.042659004660736,0.060989983229799434,12.68396810865816,0.06163746574565016,0.2599999999999998,-0.6413091039974244,0.08671190943531006,-0.43043121866220346,0.06629254545535411
+5,10,15.785400158513202,0.06263369574381074,15.943837455875455,0.06132286744850459,1.0,-0.15843729736225348,0.08765542718300515,-0.47822956746677026,0.06645712102440837
+5,8,12.34514632136168,0.05659750010868597,13.515650725321253,0.05778982270948334,-0.33000000000000007,-1.1705044039595722,0.08088844557380383,-1.1193406899953464,0.06150927270191533
+7,13 flipped,-11.063282657460709,0.05106685575240134,-12.254793279495312,0.05132247528723434,0.6699999999999999,1.191510622034602,0.07240041592453281,1.5391570931364775,0.05885229783312193
+7,14,-12.364697951117357,0.05573387607723207,-11.843163292956978,0.056548800030845746,0.2699999999999996,-0.521534658160378,0.07939793276604147,-0.7929201254446694,0.06216139611270257
+7,8,-1.8599247613999481,0.050555205819739886,-0.11435041533440979,0.05244786822225941,-0.4900000000000002,-1.7455743460655384,0.07284646674023217,-1.6915748468058203,0.05543330465485836
+7,9,-0.42064000466442114,0.054138352550401156,0.5252656635751675,0.054002723978191856,0.39999999999999947,-0.9459056682395885,0.07646734867861121,-1.141485238731108,0.06297815996433409
+8,10,2.740924236232082,0.05056681797190441,2.1917488649449584,0.05051527668713992,1.33,0.5491753712871236,0.07147584388156615,0.6411111225285762,0.06457053141982083
+9,13 flipped,-10.047883065185164,0.049782000224397174,-12.921753724567292,0.050797143544688415,0.27000000000000046,2.8738706593821277,0.07112381695776429,2.6806423318675856,0.06942862726655952
+9,15,0.35674210779718774,0.06068234114518923,0.6742916490008114,0.05937552552431238,0.17000000000000082,-0.31754954120362366,0.08489876063965479,-0.2833131599653953,0.07674043476272879

summaries/2026_apr_23/fragments/mcl1/dg_results.csv

@@ -0,0 +1,13 @@
+mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+11,O=C([O-])c1cc2c(Br)cc(Cl)cc2o1,-6.056744453098339,0.05073102886450325,-5.55
+14,Cn1c(C(=O)[O-])cc2cc(Br)ccc21,-5.575085697825291,0.05058938141916612,-5.61
+10,Cc1ccc2c(C)c(C(=O)[O-])oc2c1C,-5.832629296657866,0.0490026113302768,-5.04
+15,Cc1cccc2c(-c3ccccc3)c(C(=O)[O-])[nH]c12,-6.206963971077125,0.05681196484355936,-5.31
+2,O=C([O-])c1sc2ccccc2c1Cl,-5.396190567227687,0.03043144098709231,-5.33
+13 flipped,Cn1c(C(=O)[O-])cc2ccccc21,-3.2430084792441445,0.046463311396542153,-5.21
+3,O=C([O-])c1sc2cccc(Cl)c2c1Cl,-7.549107768563517,0.04855524023030195,-6.39
+4,O=C([O-])c1sc2cc(Cl)ccc2c1Cl,-5.626313234436136,0.04267392990221465,-5.81
+5,Cc1ccc2c(Cl)c(C(=O)[O-])sc2c1,-5.354399729191096,0.04489201507692308,-6.04
+8,Cc1c(C(=O)[O-])oc2cc(Cl)ccc12,-6.473740419186442,0.04204875278354754,-6.37
+7,Cc1c(C(=O)[O-])oc2ccc(Cl)cc12,-4.782165572380622,0.036121373926062725,-5.88
+9,Cc1c(C(=O)[O-])oc2c(C)cccc12,-5.92365081111173,0.051589678988987794,-5.48

summaries/2026_apr_23/fragments/p38/README.md

@@ -0,0 +1,40 @@
+# P38 Map
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 1.01
+- RMSE: 1.18
+- R²: 0.80
+- Kendall 𝜏: 0.47
+- Spearman ρ: 0.71
+
+## System Details
+- Ligands: 6
+- Host Atoms: 7065
+- Map Details:
+  - Edges: 10
+  - Min Dummy Atoms: 4
+  - Max Dummy Atoms: 32
+  - Mean Dummy Atoms: 19.6
+  - Median Dummy Atoms: 20.5
+
+## Simulation Details
+- TMD Sha: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427)
+- GPU: RTX 5090, RTX 50080
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 1.62 Hours
+- Average Time Per Edge: 0.16 Hours
+- Total Nanoseconds Simulated: 1438.40
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 422
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - REST: Temperature Scale 3.0
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_apr_23/fragments/p38/ddg_results.csv

@@ -0,0 +1,11 @@
+mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol)
+1_1W7H,3,35.65161204417835,0.04625444606227205,34.826259534772014,0.04703411872698075,-0.1499999999999999,0.8253525094063343,0.06596728056355936,0.9410022384411483,0.048068692888810514
+1_1W7H,5_1WBW,7.959122016788604,0.06423178357627013,9.959157669388254,0.06306211822239018,-2.0000000000000004,-2.0000356525996508,0.09001418097213083,-2.206755955167331,0.05694248966414323
+1_1W7H,6,5.321509944827347,0.07051716541002628,8.274987461101535,0.07196113367323605,-1.1,-2.9534775162741873,0.10075254526314635,-2.9642669267119293,0.05858912225565009
+4,3,38.3708634841859,0.06105890944375494,35.05070393460433,0.058894324940924336,1.3100000000000005,3.3201595495815672,0.08483355428548216,3.310460134549574,0.05144833699002701
+4,5_1WBW,10.375428814136653,0.06441129388177416,10.133045260848018,0.06459735229035656,-0.54,0.24238355328863515,0.09122298341124736,0.16270194094109502,0.059822899228904464
+4,7,9.601137864842634,0.07131624781141219,12.133188208287079,0.072266307467302,-0.8999999999999995,-2.5320503434444452,0.1015304210414661,-2.419451497942438,0.06632312191049836
+5_1WBW,3,28.53281748299989,0.06793084000926687,25.051324543581018,0.06997645920065128,1.8500000000000005,3.4814929394188705,0.09752591382102002,3.147758193608479,0.05523490382943601
+6,3,30.09464669349634,0.06841660094122753,26.499773396445338,0.06709043398831095,0.9500000000000002,3.594873297051003,0.09582253188624837,3.9052691651530775,0.05693094693208166
+6,7,2.0578751297870466,0.075261258369717,3.4723236552127186,0.07810239890546916,-1.2599999999999998,-1.4144485254256722,0.10846308923399853,-1.8246424673389345,0.07066086497842312
+7,3,29.152292375822885,0.07393697153690112,23.170254101799017,0.0711532720845785,2.21,5.982038274023866,0.10261317599797107,5.729911632492012,0.0622163308854694

summaries/2026_apr_23/fragments/p38/dg_results.csv

@@ -0,0 +1,7 @@
+mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+1_1W7H,Nc1ncccc1OCc1ccccc1,-3.2202686777337663,0.03537055105693716,-3.94
+3,c1ccc(COc2cccnc2)cc1,-2.279266439292618,0.032550320335864344,-4.09
+5_1WBW,Nc1ncccc1OCc1cccc2ccccc12,-5.427024632901097,0.04462478287991618,-5.94
+6,OCCNc1ccc(OCc2c(Cl)cccc2Cl)cn1,-6.184535604445696,0.04670770134160013,-5.04
+4,Nc1ncccc1OCc1c(Cl)cccc1Cl,-5.589726573842192,0.03984228940550477,-5.4
+7,CC(C)(CO)Nc1ccc(OCc2c(Cl)cccc2Cl)cn1,-8.00917807178463,0.05302215079457669,-6.3

summaries/2026_apr_23/jacs_set/jnk1/README.md

@@ -0,0 +1,40 @@
+# Jnk1 Map
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 1.24
+- RMSE: 1.36
+- R²: 0.55
+- Kendall 𝜏: 0.60
+- Spearman ρ: 0.75
+
+## System Details
+- Ligands: 21
+- Host Atoms: 5993
+- Map Details:
+  - Edges: 36
+  - Min Dummy Atoms: 2
+  - Max Dummy Atoms: 13
+  - Mean Dummy Atoms: 6.5
+  - Median Dummy Atoms: 6.0
+
+## Simulation Details
+- TMD Sha: [3807bc3316f1fc03f6fb7e120b900339116f2427](https://github.com/tmd-industries/tmd/tree/3807bc3316f1fc03f6fb7e120b900339116f2427)
+- GPU: RTX 5090, RTX 50080
+- MPS Processes: 2
+- Batch Mode: True
+- Total Wallclock Time: 3.46 Hours
+- Average Time Per Edge: 0.10 Hours
+- Total Nanoseconds Simulated: 3701.20
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 422
+  - Equilibration Steps: 200000
+  - Steps Per Frame: 400
+  - Production Ns: 2
+  - Target Overlap: 0.667
+  - Water Sampling: True
+  - REST: Temperature Scale 3.0
+  - Local MD: Steps 390, Radius 1.2

summaries/2026_apr_23/jacs_set/jnk1/ddg_results.csv

@@ -0,0 +1,37 @@
+mol_a,mol_b,complex_pred_dg (kcal/mol),complex_pred_dg_err (kcal/mol),solvent_pred_dg (kcal/mol),solvent_pred_dg_err (kcal/mol),exp_ddg (kcal/mol),pred_ddg (kcal/mol),pred_ddg_err (kcal/mol),mle_ddg (kcal/mol),mle_ddg_err (kcal/mol)
+17124-1,18631-1,-4.9177503280793555,0.05668730250657119,-7.319395260017533,0.05687405027963815,0.2699999999999996,2.4016449319381774,0.08030011121214167,2.461034547153657,0.06336013622209431
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+18628-1_flip,18624-1,0.02885708253989094,0.045855922245546216,0.08674642845477579,0.045915297759462355,0.20999999999999908,-0.05788934591488484,0.06489206556528825,0.14518493068598204,0.05969417801862205
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