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Remove pymbar (#268)
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* remove pymbar from analysis methods

* Fix project_analysis to always use no pymbar

* updated main project figures and csv files with no pymbar data, and used redone mcccs log-npt.txt files

* Updated figures to reflect no pymbar equilibration

* Update discussion figures to be certain no pymbar data is included

* Remake all figures and improve plotting functionality for all discussion and comparison figures

* Fix and update the plots comparing the bond distributions of flexible and fixed OH

* Turn off pymbar in lrc subproject

* Turn on monte carlo override to remove pymbar averaging for md engine data

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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CalCraven and pre-commit-ci[bot] authored Dec 6, 2024
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86 changes: 43 additions & 43 deletions reproducibility_project/aggregate_summary/aggregate_summary_all.csv
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10 changes: 5 additions & 5 deletions reproducibility_project/aggregate_summary/aggregate_summary_benzeneUA.csv
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,molecule,engine,temperature,pressure,ensemble,forcefield_name,cutoff_style,long_range_correction,r_cut,pressure-avg,pressure-std,pressure-sem,temperature-avg,temperature-std,temperature-sem,potential_energy-avg,potential_energy-std,potential_energy-sem,density-avg,density-std,density-sem
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34,benzeneUA,gomc,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,2261.3261238725845,113.57359149858733,28.393397874646833,450.0,0.0,0.0,-996248.5051899063,1104.6892172880082,276.17230432200205,0.6986877138757969,0.0008168704743399857,0.00020421761858499643
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28 changes: 14 additions & 14 deletions reproducibility_project/aggregate_summary/aggregate_summary_ethanolAA.csv
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@@ -1,19 +1,19 @@
,molecule,engine,temperature,pressure,ensemble,forcefield_name,cutoff_style,long_range_correction,r_cut,pressure-avg,pressure-std,pressure-sem,temperature-avg,temperature-std,temperature-sem,potential_energy-avg,potential_energy-std,potential_energy-sem,density-avg,density-std,density-sem
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35,ethanolAA,hoomd,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,194.85278910528027,5982.14146485386,1495.535366213465,300.0691625154075,0.22389518451464727,0.05597379612866182,-5170.099282012582,431.79370261079754,107.94842565269938,0.7941251333647472,0.0009700375981258833,0.00024250939953147083
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8 changes: 4 additions & 4 deletions reproducibility_project/aggregate_summary/aggregate_summary_methaneUA.csv
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,molecule,engine,temperature,pressure,ensemble,forcefield_name,cutoff_style,long_range_correction,r_cut,pressure-avg,pressure-std,pressure-sem,temperature-avg,temperature-std,temperature-sem,potential_energy-avg,potential_energy-std,potential_energy-sem,density-avg,density-std,density-sem
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39,methaneUA,cassandra,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1292.1047136521488,31.592770246951666,7.8981925617379165,140.0,0.0,0.0,-5695.189620521354,2.915553296563871,0.7288883241409677,0.3757235620453125,0.0001751962404427804,4.37990601106951e-05
54,methaneUA,mcccs,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1285.4831025069893,37.20743432388115,9.301858580970288,140.0,0.0,0.0,-5695.738792702148,3.029363327288005,0.7573408318220013,0.37575936057731646,0.00018371373850279828,4.592843462569957e-05
55,methaneUA,gromacs,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,13.588645423936484,1.0591647556941834,0.26479118892354586,140.00376846643206,0.051552152017493635,0.012888038004373409,-5698.862840276335,1.6907945007949114,0.42269862519872786,0.3759555197390835,5.592110954235338e-05,1.3980277385588345e-05
54,methaneUA,mcccs,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1285.4831025069893,37.20743432388115,9.301858580970288,140.0,0.0,0.0,-5695.738792702148,3.029363327288005,0.7573408318220013,0.37575936057731646,0.0001837137385027993,4.592843462569983e-05
55,methaneUA,gromacs,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,13.366359502094982,0.8733651897941064,0.2183412974485266,140.00397730808072,0.05180255592573789,0.012950638981434472,-5698.715231630187,1.0664498856306037,0.26661247140765093,0.3759573327670739,5.478411950749435e-05,1.3696029876873588e-05
8 changes: 4 additions & 4 deletions reproducibility_project/aggregate_summary/aggregate_summary_pentaneUA-constrain_bonds.csv
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,molecule,engine,temperature,pressure,ensemble,forcefield_name,cutoff_style,long_range_correction,r_cut,pressure-avg,pressure-std,pressure-sem,temperature-avg,temperature-std,temperature-sem,potential_energy-avg,potential_energy-std,potential_energy-sem,density-avg,density-std,density-sem
7,pentaneUA-constrain_bonds,gomc,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1402.1451191031786,122.33555496765892,30.58388874191473,372.0,0.0,0.0,-289476.5306132031,695.9399642321441,173.98499105803603,0.540849320879125,0.0005165323368682392,0.0001291330842170598
9,pentaneUA-constrain_bonds,gromacs,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,14.357145017690527,3.1597071853930756,0.7899267963482689,371.96957083362616,0.1266716916298173,0.03166792290745433,-2425.9794197016618,6.719675700234463,1.6799189250586157,0.5419011696532579,0.00032131570087705043,8.032892521926261e-05
23,pentaneUA-constrain_bonds,hoomd,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1384.849960890102,161.50869416714798,40.377173541786995,371.9813495927463,0.07157094608209967,0.017892736520524918,-2422.8959021289934,2.2316870527198835,0.5579217631799709,0.5416574660552227,0.00013949047379420166,3.4872618448550415e-05
32,pentaneUA-constrain_bonds,mcccs,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1405.6732120732916,62.34335707970884,15.58583926992721,372.0,0.0,0.0,-2417.163109475033,4.053145602623963,1.0132864006559907,0.5410886453415661,0.00034612068389815707,8.653017097453927e-05
48,pentaneUA-constrain_bonds,cassandra,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1348.1548122757595,70.96284002873007,17.740710007182518,372.0,0.0,0.0,-2423.008360798958,8.612346519187353,2.1530866297968383,0.541189253940625,0.0008495282868671981,0.00021238207171679952
9,pentaneUA-constrain_bonds,gromacs,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,13.719782841107865,2.4999849573567596,0.6249962393391899,371.96862981453387,0.12374673503118365,0.030936683757795912,-2424.841930856993,3.7319849756230785,0.9329962439057696,0.5419106091623472,0.00029295398113316184,7.323849528329046e-05
23,pentaneUA-constrain_bonds,hoomd,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1401.0486089437786,121.70542529812478,30.426356324531195,371.977824827842,0.060515859399537374,0.015128964849884343,-2422.405495644851,1.8321299305191419,0.45803248262978546,0.5416387978239146,0.00013790426503226062,3.4476066258065156e-05
32,pentaneUA-constrain_bonds,mcccs,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1405.6732120732916,62.34335707970884,15.58583926992721,372.0,0.0,0.0,-2417.163109475033,4.0531456026239985,1.0132864006559996,0.5410886453415661,0.0003461206838981674,8.653017097454186e-05
48,pentaneUA-constrain_bonds,cassandra,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1348.1548122757595,70.96284002873008,17.74071000718252,372.0,0.0,0.0,-2423.008360798958,8.612346519187353,2.1530866297968383,0.541189253940625,0.0008495282868671981,0.00021238207171679952
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