Add Summaries for Water Box Change

summaries/2026_mar_25/README.md

@@ -0,0 +1,13 @@
+# Summary
+- Number of Datasets: 14
+- Number of Ligands: 353
+- Number of Edges: 607
+- Total Wallclock Time: 351.11 Hours
+- Average Time Per Edge: 0.58 Hours
+- TMD Sha: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e)
+
+![Retrospective dG performance](dg_plot.png)
+
+## Notes:
+- A subset of the datasets run with dynamically sized water boxes (https://github.com/tmd-industries/tmd/pull/94)
+- Wallclock time for some datasets is off due to running out of disk space during the intitial run

summaries/2026_mar_25/fragments/mcl1/README.md

@@ -0,0 +1,39 @@
+# Mcl1 Map
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 0.55
+- RMSE: 0.72
+- R²: 0.26
+- Kendall 𝜏: 0.27
+- Spearman ρ: 0.38
+
+## 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: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e)
+- GPU: RTX 4090
+- MPS Processes: 12
+- Total Wallclock Time: 3.62 Hours
+- Average Time Per Edge: 0.18 Hours
+- Total Nanoseconds Simulated: 2007.40
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 4115
+  - 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_mar_25/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)
+10,15,5.414377300351039,0.06457087607262701,4.92091090597578,0.0595328048242698,-0.2699999999999996,0.49346639437525996,0.08782683466362179,0.3735861800011282,0.07390970286288413
+11,14,-0.32393759803494127,0.06288918326083696,-1.324761245045128,0.06242950099429511,-0.0600000000000005,1.0008236470101868,0.0886142875929826,1.001357518526012,0.0730428425216689
+2,13 flipped,9.805732856989476,0.054769429939795035,7.621378216978718,0.05438437274791764,0.1200000000000001,2.184354640010759,0.07718387432044703,1.7684387338892846,0.05478833777010601
+2,14,7.3815780392442285,0.06608764128091692,7.200699304390168,0.06446121604375969,-0.28000000000000025,0.18087873485406022,0.09231914592280095,-0.016147151056110864,0.05403385777115431
+2,15,19.613284678014328,0.07223852553659298,20.50615185340026,0.06899544333964779,0.020000000000000462,-0.8928671753859327,0.09989382249836844,-0.24129258901693174,0.0598540791976062
+2,3,0.49952108975603976,0.04307962616632179,2.2674712478375794,0.04501217819894488,-1.0599999999999996,-1.7679501580815398,0.06230529974924771,-1.765625643061684,0.05826086956679544
+2,4,-4.37090664544144,0.04177609693964057,-3.757010616181308,0.041144244576848954,-0.47999999999999954,-0.6138960292601318,0.05863523801699633,-0.615721012828609,0.052101439785242454
+2,5,-0.019201811794486236,0.043628111657551906,0.11172939014493247,0.042998621401803584,-0.71,-0.1309312019394187,0.06125596762160777,-0.027484250042722813,0.052642991925706636
+3,11,7.061484126893448,0.06217221406725052,6.287833170504798,0.062276228225281643,0.8399999999999999,0.7736509563886494,0.08799836818936695,0.7481209734795611,0.0762228835763325
+3,4,-4.825160975104707,0.05331762713971417,-5.953344337159753,0.05227793059282051,0.5800000000000001,1.1281833620550463,0.07467095413129085,1.1499046302330749,0.06613194487722354
+4,11,11.888021595957087,0.060772895251744063,12.315351929632866,0.06244089912200412,0.2599999999999998,-0.427330333675779,0.08713329260646444,-0.4017836567535138,0.07162512887044067
+5,10,15.08389166215939,0.06014287882741134,15.595605345656667,0.0627537583508613,1.0,-0.5117136834972758,0.08692065382178725,-0.5873945189753371,0.06820130482312287
+5,8,11.987033373391197,0.05662648514473795,13.1200772108599,0.0556392701067972,-0.33000000000000007,-1.1330438374687042,0.07938694601673732,-0.896165788533744,0.06078155659513949
+7,13 flipped,-4.599529250990518,0.04927927086874049,-5.888689748339937,0.04640034044784516,0.6699999999999999,1.2891604973494197,0.06768632159477002,1.3666028580020844,0.05728718438418723
+7,14,-6.660551378692329,0.053833501880447755,-6.109615722513587,0.05357332488864938,0.2699999999999996,-0.5509356561787419,0.07594831837728173,-0.41798302694331113,0.0565660439193866
+7,8,-1.3617545102866675,0.050159285792232555,-0.2467185559614011,0.04863832730667633,-0.4900000000000002,-1.1150359543252664,0.06986874003714565,-1.325485914463667,0.05420910790102557
+7,9,0.2353244277111983,0.053960713541693864,0.8500609769167551,0.053147374272155004,0.39999999999999947,-0.6147365492055568,0.07573903879739476,-0.5966236319216067,0.061583563539376114
+8,10,3.1066804788163846,0.05083630810495768,2.7706628132414557,0.04845238413245525,1.33,0.3360176655749291,0.07022794137564611,0.30877126955840684,0.06736988363545615
+9,13 flipped,-4.945964936863256,0.048560721718424585,-6.656673208935519,0.04913519870363419,0.27000000000000046,1.7107082720722626,0.06908264214301511,1.963226489923691,0.06912874147294089
+9,15,6.713363667695627,0.059270174271688084,6.428617724078294,0.056078033885336824,0.17000000000000082,0.2847459436173325,0.08159472680658512,-0.04650483298252528,0.07320882281948528

summaries/2026_mar_25/fragments/mcl1/dg_results.csv

@@ -0,0 +1,13 @@
+mol,smiles,pred_dg (kcal/mol),pred_dg_err (kcal/mol),exp_dg (kcal/mol)
+10,Cc1ccc2c(C)c(C(=O)[O-])oc2c1C,-6.012643996564674,0.05242004186617595,-5.04
+15,Cc1cccc2c(-c3ccccc3)c(C(=O)[O-])[nH]c12,-5.639057816563546,0.05210358325516762,-5.31
+11,O=C([O-])c1cc2c(Br)cc(Cl)cc2o1,-6.415269897128737,0.05730031820659568,-5.55
+14,Cn1c(C(=O)[O-])cc2cc(Br)ccc21,-5.413912378602725,0.04529823812322287,-5.61
+2,O=C([O-])c1sc2ccccc2c1Cl,-5.397765227546614,0.029457213183957706,-5.33
+13 flipped,Cn1c(C(=O)[O-])cc2ccccc21,-3.6293264936573295,0.04619561177261422,-5.21
+3,O=C([O-])c1sc2cccc(Cl)c2c1Cl,-7.163390870608298,0.05026531124059632,-6.39
+4,O=C([O-])c1sc2cc(Cl)ccc2c1Cl,-6.013486240375223,0.042974790507111414,-5.81
+5,Cc1ccc2c(Cl)c(C(=O)[O-])sc2c1,-5.425249477589337,0.043629774126448126,-6.04
+8,Cc1c(C(=O)[O-])oc2cc(Cl)ccc12,-6.321415266123081,0.042318322648744744,-6.37
+7,Cc1c(C(=O)[O-])oc2ccc(Cl)cc12,-4.995929351659414,0.033879004525247954,-5.88
+9,Cc1c(C(=O)[O-])oc2c(C)cccc12,-5.592552983581021,0.05142711687997495,-5.48

summaries/2026_mar_25/fragments/p38/README.md

@@ -0,0 +1,39 @@
+# P38 Map
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 0.76
+- RMSE: 0.87
+- R²: 0.89
+- Kendall 𝜏: 0.73
+- Spearman ρ: 0.89
+
+## 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: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e)
+- GPU: RTX 4090
+- MPS Processes: 12
+- Total Wallclock Time: 3.68 Hours
+- Average Time Per Edge: 0.37 Hours
+- Total Nanoseconds Simulated: 1327.20
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 4115
+  - 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_mar_25/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,3,24.430898761678122,0.04788938647581076,23.76076092448228,0.04887164003735272,-0.1499999999999999,0.6701378371958422,0.06842390325734234,0.6698770401310097,0.04774679250108025
+1_1W7H,5_1WBW,7.2286107581426196,0.0635611147734271,9.553458900345417,0.06147948374421008,-2.0000000000000004,-2.324848142202797,0.08842930641306289,-2.4672171284341453,0.05628380518080255
+1_1W7H,6,3.0290489275099204,0.06864172836091006,5.39164764945018,0.07126660798281463,-1.1,-2.3625987219402593,0.09894754310112579,-2.18380193014417,0.05775252723087723
+4,3,27.816111505983635,0.05843091334780482,24.627815710607177,0.057923315699726176,1.3100000000000005,3.18829579537646,0.0822756472858696,3.589054222024915,0.05039019046097695
+4,5_1WBW,10.512071006802866,0.06416426878289874,10.283943686233378,0.061487730520289566,-0.54,0.22812732056948767,0.08886953579815651,0.45196005345975987,0.05854299126439352
+4,7,9.558682032897066,0.07184021927010815,9.809233392132136,0.07004325382212585,-0.8999999999999995,-0.2505513592350693,0.10033481205826802,-1.1318600091010582,0.06454740357452685
+5_1WBW,3,17.091420698806427,0.0685147115459836,14.046813133546074,0.06656850249210051,1.8500000000000005,3.0446075652603524,0.09552816978394452,3.137094168565155,0.054095801780668744
+6,3,20.9553543722249,0.06529752891043908,18.407732057334012,0.065342732401627,0.9500000000000002,2.5476223148908868,0.09237662019970348,2.8536789702751797,0.05562232866588817
+6,7,2.639382360861954,0.07620949660699415,4.308814210568148,0.07367972820131477,-1.2599999999999998,-1.6694318497061933,0.10600278166591229,-1.8672352608507934,0.06870982069351798
+7,3,20.281579229291463,0.06899997841436346,14.56095953919259,0.06889615633299423,2.21,5.720619690098874,0.09750731961572427,4.720914231125973,0.06054288771047669

summaries/2026_mar_25/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,-3.293107268110638,0.03550540205009898,-3.94
+3,c1ccc(COc2cccnc2)cc1,-2.6232302279796285,0.03192369996416519,-4.09
+5_1WBW,Nc1ncccc1OCc1cccc2ccccc12,-5.7603243965447835,0.04367188055134978,-5.94
+6,OCCNc1ccc(OCc2c(Cl)cccc2Cl)cn1,-5.476909198254808,0.04554910346882849,-5.04
+4,Nc1ncccc1OCc1c(Cl)cccc1Cl,-6.212284450004543,0.03898780162168024,-5.4
+7,CC(C)(CO)Nc1ccc(OCc2c(Cl)cccc2Cl)cn1,-7.3441444591056015,0.05144238168010253,-6.3

summaries/2026_mar_25/jacs_set/jnk1/README.md

@@ -0,0 +1,39 @@
+# Jnk1 Map
+
+![Retrospective dG performance](dg_plot.png)
+
+## Statistics Summary
+- MUE: 1.23
+- RMSE: 1.36
+- R²: 0.53
+- Kendall 𝜏: 0.58
+- Spearman ρ: 0.73
+
+## 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: [d90311ea6b8fd4d5bddae32b2925ef72d57ec45e](https://github.com/tmd-industries/tmd/tree/d90311ea6b8fd4d5bddae32b2925ef72d57ec45e)
+- GPU: RTX 4090
+- MPS Processes: 12
+- Total Wallclock Time: 7.10 Hours
+- Average Time Per Edge: 0.20 Hours
+- Total Nanoseconds Simulated: 3245.60
+- TMD Forcefield: smirnoff_2_0_0_amber_am1bcc.py
+- Ligand Charges: Amber AM1BCC ELF10
+- Simulation Details:
+  - Seed: 4115
+  - 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_mar_25/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,-3.8647727515714645,0.054885792932781126,-5.835118787534282,0.05560481578007555,0.2699999999999996,1.9703460359628173,0.07813031296363958,2.093299213377218,0.061833957222889126
+17124-1,18637-1,-8.737563809900557,0.05878238191556125,-8.64116002762175,0.059117852092238625,-0.46000000000000085,-0.09640378227880807,0.08336839244981702,-0.3621144989218372,0.07502603953294852
+17124-1,18652-1,-15.852860768562692,0.05806034019583097,-14.544529721057774,0.05733720936193133,-1.0,-1.3083310475049175,0.08159999191831806,-1.228035812513827,0.07424175296587847
+17124-1,18660-1,-31.88404273447657,0.06608770834881084,-30.889896137345854,0.06287393302529407,0.9800000000000004,-0.9941465971307155,0.09121796231481301,-0.943978430249512,0.07609020972881556
+18626-1,18628-1_flip,2.2741472007944403,0.0520658035238181,0.984869809769274,0.04912496288301538,0.16999999999999993,1.2892773910251665,0.07158288814261736,1.2084999712534037,0.07009132013656763
+18626-1,18632-1,3.276894059177301,0.04791786697446508,3.4860346493206076,0.047568399397961744,-0.21000000000000085,-0.2091405901433071,0.0675194386578157,-0.10424604501787638,0.06545060218363828
+18626-1,18635-1,2.513395425723552,0.05164182476788772,1.5727088262146292,0.047601346833060776,1.5799999999999992,0.9406865995089229,0.07023365493606729,0.9049502744611946,0.07108359210912678
+18627-1,18625-1,-1.3854766128047464,0.050789720304911815,-1.7574254511080591,0.050682974971846324,0.370000000000001,0.37194883830331277,0.07175207063665809,0.26824354919884286,0.07112979610140045
+18627-1,18630-1,1.170877667593746,0.03454804175703692,0.8726610927377247,0.035744889895331526,-0.6600000000000001,0.29821657485602127,0.04971181291076941,0.39511807225177975,0.06571545452948217
+18627-1,18633-1,2.9729711523782902,0.04794810612593841,2.8629061370881788,0.04793986152248772,-0.6899999999999995,0.1100650152901116,0.0678030324090269,0.022404909560573394,0.07031702849420254
+18628-1_flip,18624-1,-1.081141378936168,0.04563799453537001,-0.7559867426234538,0.04495635808420401,0.20999999999999908,-0.32515463631271424,0.06406169430639216,-0.4053172400691647,0.058509651034385865
+18628-1_flip,18625-1,-4.114919805538485,0.05625536308469383,-3.083438191185624,0.051831901898329605,0.5899999999999999,-1.0314816143528616,0.0764932149290955,-1.009427898480916,0.06871423837404882
+18629-1,18624-1,0.3578309613775808,0.0441654178648519,-0.11620245894064767,0.044648617298344365,0.17999999999999972,0.4740334203182285,0.06280193597199846,0.5167842295567269,0.06022848028194439
+18629-1,18635-1,1.414187756891768,0.047990580543108556,0.6904630501382738,0.046518433375926614,1.38,0.7237247067534943,0.06683607158275472,0.6185517728336825,0.07017478870001749
+18629-1,18636-1,-4.3070934664376095,0.052833393917836924,-3.13411826297216,0.05147655057325953,1.1600000000000001,-1.17297520346545,0.073764508890107,-1.1038453891554205,0.07061765517570645
+18630-1,18624-1,0.5512678480879679,0.0432424902693843,0.12849686015841913,0.04489923793910743,0.6500000000000004,0.4227709879295488,0.06233662272059965,0.4772361353588144,0.053139179543399064
+18630-1,18633-1,1.6743118983035528,0.04044484567931198,2.1251539352542133,0.0382776233613621,-0.02999999999999936,-0.45084203695066055,0.05568628190333463,-0.37271316269120636,0.06330147151949378
+18631-1,18624-1,2.6350959600605415,0.05351905742470859,1.0018514976943491,0.050160144140371656,0.9199999999999999,1.6332444623661924,0.07335072983830575,1.7920110711599726,0.04936671517364012
+18631-1,18625-1,-0.8811205276604722,0.04935500894238074,-1.9873721301762677,0.050502368075055044,1.3000000000000007,1.1062516025157954,0.07061448922771318,1.1879004127482213,0.06111742679625265
+18632-1,18624-1,-1.5437239207346387,0.04719190407889437,-2.5563353822406367,0.04869548269677142,0.5899999999999999,1.012611461505998,0.06781095667857173,0.9074287762021154,0.05286177666215614
+18633-1,18624-1,-0.9738215656983182,0.049322860317631244,-1.7947668493830655,0.04796851198915113,0.6799999999999997,0.8209452836847473,0.06880205441966031,0.8499492980500207,0.05873445270693901
+18634-1,18631-1,-2.8077079337406805,0.04779418902419944,-4.659114138962926,0.049819987980265705,0.5800000000000001,1.8514062052222457,0.06903850886885322,1.9740963458066787,0.049007742217021893
+18634-1,18632-1,1.7264524480982395,0.050496179910048934,-1.3581658167952537,0.04872773416201176,0.9100000000000001,3.0846182648934932,0.07017304512468955,2.858678640764536,0.05252669475661339
+18634-1,18637-1,-9.391913299563647,0.059648770926641545,-8.74506422642863,0.057624685262292544,-0.15000000000000036,-0.6468490731350177,0.08293720651575645,-0.48131736649237666,0.06486314160883315
+18634-1,18658-1,-4.769778807170652,0.040561714573675585,-5.227230618912992,0.04121419704990284,0.2900000000000009,0.4574518117423392,0.05782614225092788,0.29993137723099217,0.058345747860679725
+18636-1,18624-1,4.322044652827047,0.052358806810158746,2.6044886616656897,0.05116999856492054,-0.9800000000000004,1.7175559911613565,0.07321074650430424,1.6206296187121474,0.06021474425951163
+18636-1,18635-1,5.975757630044046,0.04927014025484662,4.403131996849364,0.04936533622437404,0.21999999999999975,1.572625633194682,0.06974584676722875,1.722397161989103,0.07016299992344914
+18638-1,18634-1,19.933161219169854,0.05474680057247788,19.333902787551228,0.055055744327736106,0.09999999999999964,0.5992584316186267,0.07764243141738743,0.5865602573261377,0.06567159575328169
+18638-1,18639-1,76.11103142952916,0.06641119486511565,76.40873201939952,0.06602431482034594,0.34999999999999964,-0.2977005898703481,0.09364644654715157,-0.3073263900654428,0.08535810519136512
+18638-1,18652-1,5.079170833530567,0.04696269626969517,5.853618640138438,0.045738574313910714,-0.5899999999999999,-0.7744478066078717,0.06555541183753462,-0.7606784227582288,0.0787852295957273
+18639-1,18637-1,-75.50232077851742,0.0642314590962166,-75.79945877296186,0.06342839482095378,-0.40000000000000036,0.2971379944444523,0.09027093445396331,0.41256928089920386,0.08473768212811376
+18639-1,18652-1,-71.09661386070216,0.07181965975356393,-70.79714638650498,0.07017222405162754,-0.9399999999999995,-0.2994674741971809,0.10041018153289787,-0.453352032692786,0.08404407205682159
+18658-1,18660-1,-26.2730920700312,0.06257238258073217,-25.025495255023163,0.061581523656143,1.0,-1.2475968150080372,0.08779286484471056,-1.3631126750510436,0.07467571452768058
+18659-1,18634-1,0.055861584825455904,0.05250120827854113,0.2339738965668692,0.050037742841646124,-0.5199999999999996,-0.1781123117414133,0.07252690934676222,-0.39418895491917283,0.06177552868043656
+18659-1,18658-1,-5.998076434402388,0.054096477136386496,-5.715596054821781,0.054162279062720114,-0.22999999999999865,-0.2824803795806074,0.07655051477185217,-0.09425757768818066,0.0708846791346618
+18659-1,18660-1,-22.190955378068008,0.06067754549431937,-20.66968130351767,0.05875341542147397,0.7700000000000014,-1.5212740745503384,0.08446140154474997,-1.4573702527392243,0.07738508894189546