diff --git a/Ranking/SYSTEM_FormFactor_Ranking.json b/Ranking/SYSTEM_FormFactor_Ranking.json index 16d8f97a1..cd6bc658d 100644 --- a/Ranking/SYSTEM_FormFactor_Ranking.json +++ b/Ranking/SYSTEM_FormFactor_Ranking.json @@ -173,7 +173,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [32, 32] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 4000 }, @@ -442,7 +442,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [32, 32] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 3200 } @@ -661,7 +661,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [128, 128] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 16000 }, @@ -719,7 +719,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [512, 512] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 64000 }, @@ -993,7 +993,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [128, 128] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 12800 } @@ -1046,7 +1046,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [512, 512] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 51200 } @@ -1149,7 +1149,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [32, 32] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 3600 }, @@ -2072,6 +2072,7 @@ "TotalQuality": { "headgroup": 0.620293, "tails": 0.728064, "total": 0.69214, "FFQuality": 0.455 }, "system": { "DOI": "10.5281/zenodo.166034", + "AUTHORS_CONTACT": "Favela-Rosales, Fernando", "SYSTEM": "POPC_T298K", "SOFTWARE": "gromacs", "FF": "Slipids", @@ -2126,7 +2127,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [512, 512] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 57600 }, @@ -2184,7 +2185,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [128, 128] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 14400 }, @@ -5246,6 +5247,7 @@ "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, "ID": 797, + "AUTHORS_CONTACT": "Hoeflich, Julianne", "path": "4f5/fb4/4f5fb4c911390b50b56d06364c85910c10191c57/ea16a8b51b9d71838d911eb3cebbc69ad05600d8/" } }, @@ -5344,6 +5346,7 @@ "TRJLENGTH": 500010, "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 428, + "AUTHORS_CONTACT": "Buslaev Pavel", "path": "b4f/866/b4f866c0dabffa6cd891e91841591d46590f34aa/a231c358dd8c0b7bb4cf558ccdbf022373354a9a/" } }, @@ -6144,6 +6147,7 @@ "TRJLENGTH": 300100, "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 558, + "AUTHORS_CONTACT": "Papadopoulos, Chris; Fuchs, Patrick F.J.", "path": "a63/ca7/a63ca7001cbd5cfc328da122668d1aebc00f2c91/220540156a6ac7813942fd01d998a491b6ff9b8b/" } }, @@ -6513,6 +6517,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 430, + "AUTHORS_CONTACT": "Javanainen, Matti", "path": "2d4/61b/2d461bc9d828af155146162ef42438974e4cbeaf/c8ce4cc36ef6ec7a085cf011176a92d9d746a792/" } }, @@ -6552,6 +6557,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 0, "DOI": "10.5281/zenodo.14066", + "AUTHORS_CONTACT": "Santuz, Hubert", "TRAJECTORY_SIZE": 902127456, "TPR": [ ["POPC_0CHL.tpr"] @@ -6561,7 +6567,6 @@ "CAL": "CA", "SOD": "NA", "TRJLENGTH": 150700, - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 612, "path": "edf/8a8/edf8a82ed02a87f84c14b740c90dfa718d3f7f8b/1048c4444299bb5adb360e7e17df2b616ab7a4fc/" } @@ -6738,6 +6743,7 @@ "TotalQuality": { "headgroup": 0.556067, "tails": 0.567598, "total": 0.563754, "FFQuality": 1.355 }, "system": { "DOI": "10.5281/zenodo.15021844", + "AUTHORS_CONTACT": "Hoeflich, Julianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -7297,7 +7303,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [128, 128] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 20800 }, @@ -7355,7 +7361,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [512, 512] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 83200 }, @@ -7402,6 +7408,8 @@ "TotalQuality": { "headgroup": 0.11395, "tails": 0.709066, "total": 0.510694, "FFQuality": 1.555 }, "system": { "DOI": "10.5281/zenodo.14713793", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", + "FF": "Sage 2.2.1", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -7415,7 +7423,7 @@ "POPC": { "NAME": "POPC", "MAPPING": "mappingPOPCsage_smiles.yaml", - "COUNT": [128, 0] + "COUNT": [64, 64] }, "SOL": { "NAME": "TIP3P", "MAPPING": "mappingTIP3Psage_smiles.yaml", "COUNT": 5120 } }, @@ -7423,7 +7431,6 @@ "TOP": [ ["bilayer.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 612503984, "TRJLENGTH": 500100, "TEMPERATURE": 300, @@ -7563,7 +7570,7 @@ "COMPOSITION": { "POPE": { "NAME": "PE", - "MAPPING": "mappingPOPElipid17.yaml", + "MAPPING": "mappingPOPE_AmberLipid.yaml", "COUNT": [250, 250] }, "SOL": { "NAME": "WAT", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 25000 } @@ -7769,6 +7776,7 @@ "TotalQuality": { "headgroup": 0.529893, "tails": 0.177282, "total": 0.294819, "FFQuality": 1.645 }, "system": { "DOI": "10.5281/zenodo.15002801", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -7793,7 +7801,6 @@ "TOP": [ ["bilayer5.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 414960964, "TRJLENGTH": 338800, "TEMPERATURE": 300, @@ -7815,6 +7822,7 @@ "TotalQuality": { "headgroup": 0.249069, "tails": 0.0209952, "total": 0.0970196, "FFQuality": 1.677 }, "system": { "DOI": "10.5281/zenodo.10467181", + "AUTHORS_CONTACT": "Nencini, Ricky", "TRJ": [ ["POPS_144_144_Na_contraions_prosECCo75.xtc"] ], @@ -8154,6 +8162,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 400, "DOI": "10.5281/zenodo.1129415", + "AUTHORS_CONTACT": "Piggot, Thomas", "TRAJECTORY_SIZE": 221970700, "TPR": [ ["for-md-CHARMM36_POPS_298K_v2.tpr"] @@ -8161,7 +8170,6 @@ "TRJ": [ ["md-CHARMM36_10A-switch_POPS_v2_400-500ns_skip10.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 5, "path": "1b2/6e6/1b26e6c750b4f39c37770422cd4d3c40240cf111/995bc873b811ca09c916b47784fa33bb9d793732/" } @@ -8182,7 +8190,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [32, 32] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 5200 }, @@ -8611,6 +8619,7 @@ "TotalQuality": { "headgroup": 0.476603, "tails": 0.176768, "total": 0.276713, "FFQuality": 1.845 }, "system": { "DOI": "10.5281/zenodo.15002712", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -8635,7 +8644,6 @@ "TOP": [ ["bilayer2.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 350763692, "TRJLENGTH": 286400, "TEMPERATURE": 300, @@ -9261,6 +9269,7 @@ "TotalQuality": { "headgroup": 0.117569, "tails": 0.44331, "total": 0.334729, "FFQuality": 2.155 }, "system": { "DOI": "10.5281/zenodo.15065748", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -9453,6 +9462,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 106, + "AUTHORS_CONTACT": "Thomas Piggot", "path": "f40/bb6/f40bb6ab5d44402be07059e8df74b5a8200f031e/6774168dfec0a5a7377c8a46341eba603f320cf7/" } }, @@ -9893,7 +9903,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [512, 512] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 96000 }, @@ -10170,7 +10180,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [128, 128] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 24000 }, @@ -10228,7 +10238,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [32, 32] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 6000 }, @@ -10275,6 +10285,8 @@ "TotalQuality": { "headgroup": 0.549462, "tails": 0.310135, "total": 0.389911, "FFQuality": 2.355 }, "system": { "DOI": "10.5281/zenodo.14713771", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", + "FF": "Sage 2.2.1", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -10288,7 +10300,7 @@ "POPC": { "NAME": "POPC", "MAPPING": "mappingPOPCsage_smiles.yaml", - "COUNT": [128, 0] + "COUNT": [64, 64] }, "SOL": { "NAME": "TIP3P", "MAPPING": "mappingTIP3Psage_smiles.yaml", "COUNT": 5120 } }, @@ -10366,6 +10378,7 @@ "TotalQuality": { "headgroup": 0.536115, "tails": 0.199196, "total": 0.311503, "FFQuality": 3.045 }, "system": { "DOI": "10.5281/zenodo.15065566", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -10549,6 +10562,7 @@ }, "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "path": "e2b/09a/e2b09acaead3655073b4ed768e4a08d879b0042d/bb294604ef4b17df4b59195e2ac600630d33c644/" } }, @@ -10595,6 +10609,7 @@ }, "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "path": "58d/654/58d654af9894439448a86b0c7a9f13020d41d54d/afaaae028c976185c3ce34198181af80a226d37f/" } } diff --git a/Ranking/SYSTEM_headgroup_Ranking.json b/Ranking/SYSTEM_headgroup_Ranking.json index d2b61c3b0..f73b7c4af 100644 --- a/Ranking/SYSTEM_headgroup_Ranking.json +++ b/Ranking/SYSTEM_headgroup_Ranking.json @@ -759,6 +759,7 @@ "TRJLENGTH": 300100, "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 558, + "AUTHORS_CONTACT": "Papadopoulos, Chris; Fuchs, Patrick F.J.", "path": "a63/ca7/a63ca7001cbd5cfc328da122668d1aebc00f2c91/220540156a6ac7813942fd01d998a491b6ff9b8b/" } }, @@ -1777,6 +1778,7 @@ "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, "ID": 797, + "AUTHORS_CONTACT": "Hoeflich, Julianne", "path": "4f5/fb4/4f5fb4c911390b50b56d06364c85910c10191c57/ea16a8b51b9d71838d911eb3cebbc69ad05600d8/" } }, @@ -1890,6 +1892,7 @@ "TotalQuality": { "headgroup": 0.620293, "tails": 0.728064, "total": 0.69214, "FFQuality": 0.455 }, "system": { "DOI": "10.5281/zenodo.166034", + "AUTHORS_CONTACT": "Favela-Rosales, Fernando", "SYSTEM": "POPC_T298K", "SOFTWARE": "gromacs", "FF": "Slipids", @@ -2347,7 +2350,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [512, 512] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 51200 } @@ -2497,6 +2500,7 @@ "TotalQuality": { "headgroup": 0.556067, "tails": 0.567598, "total": 0.563754, "FFQuality": 1.355 }, "system": { "DOI": "10.5281/zenodo.15021844", + "AUTHORS_CONTACT": "Hoeflich, Julianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -2555,7 +2559,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [128, 128] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 12800 } @@ -2596,6 +2600,8 @@ "TotalQuality": { "headgroup": 0.549462, "tails": 0.310135, "total": 0.389911, "FFQuality": 2.355 }, "system": { "DOI": "10.5281/zenodo.14713771", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", + "FF": "Sage 2.2.1", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -2609,7 +2615,7 @@ "POPC": { "NAME": "POPC", "MAPPING": "mappingPOPCsage_smiles.yaml", - "COUNT": [128, 0] + "COUNT": [64, 64] }, "SOL": { "NAME": "TIP3P", "MAPPING": "mappingTIP3Psage_smiles.yaml", "COUNT": 5120 } }, @@ -2727,6 +2733,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 430, + "AUTHORS_CONTACT": "Javanainen, Matti", "path": "2d4/61b/2d461bc9d828af155146162ef42438974e4cbeaf/c8ce4cc36ef6ec7a085cf011176a92d9d746a792/" } }, @@ -2735,6 +2742,7 @@ "TotalQuality": { "headgroup": 0.536115, "tails": 0.199196, "total": 0.311503, "FFQuality": 3.045 }, "system": { "DOI": "10.5281/zenodo.15065566", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -2781,6 +2789,7 @@ "TotalQuality": { "headgroup": 0.529893, "tails": 0.177282, "total": 0.294819, "FFQuality": 1.645 }, "system": { "DOI": "10.5281/zenodo.15002801", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -2805,7 +2814,6 @@ "TOP": [ ["bilayer5.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 414960964, "TRJLENGTH": 338800, "TEMPERATURE": 300, @@ -2916,6 +2924,7 @@ }, "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "path": "e2b/09a/e2b09acaead3655073b4ed768e4a08d879b0042d/bb294604ef4b17df4b59195e2ac600630d33c644/" } }, @@ -2936,7 +2945,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [32, 32] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 3200 } @@ -2977,6 +2986,7 @@ "TotalQuality": { "headgroup": 0.476603, "tails": 0.176768, "total": 0.276713, "FFQuality": 1.845 }, "system": { "DOI": "10.5281/zenodo.15002712", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -3001,7 +3011,6 @@ "TOP": [ ["bilayer2.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 350763692, "TRJLENGTH": 286400, "TEMPERATURE": 300, @@ -3315,6 +3324,7 @@ }, "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "path": "58d/654/58d654af9894439448a86b0c7a9f13020d41d54d/afaaae028c976185c3ce34198181af80a226d37f/" } }, @@ -3562,6 +3572,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 400, "DOI": "10.5281/zenodo.1129415", + "AUTHORS_CONTACT": "Piggot, Thomas", "TRAJECTORY_SIZE": 221970700, "TPR": [ ["for-md-CHARMM36_POPS_298K_v2.tpr"] @@ -3569,7 +3580,6 @@ "TRJ": [ ["md-CHARMM36_10A-switch_POPS_v2_400-500ns_skip10.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 5, "path": "1b2/6e6/1b26e6c750b4f39c37770422cd4d3c40240cf111/995bc873b811ca09c916b47784fa33bb9d793732/" } @@ -3579,6 +3589,7 @@ "TotalQuality": { "headgroup": 0.249069, "tails": 0.0209952, "total": 0.0970196, "FFQuality": 1.677 }, "system": { "DOI": "10.5281/zenodo.10467181", + "AUTHORS_CONTACT": "Nencini, Ricky", "TRJ": [ ["POPS_144_144_Na_contraions_prosECCo75.xtc"] ], @@ -3933,6 +3944,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 106, + "AUTHORS_CONTACT": "Thomas Piggot", "path": "f40/bb6/f40bb6ab5d44402be07059e8df74b5a8200f031e/6774168dfec0a5a7377c8a46341eba603f320cf7/" } }, @@ -4416,6 +4428,7 @@ "TotalQuality": { "headgroup": 0.117569, "tails": 0.44331, "total": 0.334729, "FFQuality": 2.155 }, "system": { "DOI": "10.5281/zenodo.15065748", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -4512,6 +4525,8 @@ "TotalQuality": { "headgroup": 0.11395, "tails": 0.709066, "total": 0.510694, "FFQuality": 1.555 }, "system": { "DOI": "10.5281/zenodo.14713793", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", + "FF": "Sage 2.2.1", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -4525,7 +4540,7 @@ "POPC": { "NAME": "POPC", "MAPPING": "mappingPOPCsage_smiles.yaml", - "COUNT": [128, 0] + "COUNT": [64, 64] }, "SOL": { "NAME": "TIP3P", "MAPPING": "mappingTIP3Psage_smiles.yaml", "COUNT": 5120 } }, @@ -4533,7 +4548,6 @@ "TOP": [ ["bilayer.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 612503984, "TRJLENGTH": 500100, "TEMPERATURE": 300, @@ -4765,7 +4779,7 @@ "COMPOSITION": { "POPE": { "NAME": "PE", - "MAPPING": "mappingPOPElipid17.yaml", + "MAPPING": "mappingPOPE_AmberLipid.yaml", "COUNT": [250, 250] }, "SOL": { "NAME": "WAT", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 25000 } @@ -5545,7 +5559,7 @@ "POPC": { "NAME": "PC", "MOLTYPE": "system1", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [76, 74] }, "POPG": { @@ -5634,6 +5648,7 @@ "FORMFACTOR": [] }, "ID": 307, + "AUTHORS_CONTACT": "Javanainen, Matti", "path": "c74/6ca/c746ca52b71d685e53a802e8046e1253baf6af2b/8850a90345eb033df4ae3228c3b9fa1fbbe40162/" } }, @@ -5684,6 +5699,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 58, + "AUTHORS_CONTACT": "Kiirikki, M. Anne; Ollila O. H. Samuli", "path": "be6/5d5/be65d56aa0b9732c1f75b8e2de40133ac6c5f706/fe08222fa3d4cc603161b05233be0af37dd3cc8b/" } }, @@ -5725,6 +5741,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 100, "DOI": "10.5281/zenodo.3997116", + "AUTHORS_CONTACT": "Kiirikki, M. Anne; Ollila, O. H. Samuli", "TRAJECTORY_SIZE": 7413293748, "TPR": [ ["run_400ns.tpr"] @@ -5732,7 +5749,6 @@ "TRJ": [ ["100-400ns.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 592, "path": "0c2/1a9/0c21a9be136ea0eb9df9e5c6cdc19f723a0af245/9ac73b6a98acb54a7a67a5d690794ad7f1e4a1d1/" } @@ -5775,6 +5791,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 0, "DOI": "10.5281/zenodo.3859339", + "AUTHORS_CONTACT": "Ollila, O.H.Samuli; Virtanen, I.Salla", "TRAJECTORY_SIZE": 8278576984, "TPR": [ ["topol.tpr"] @@ -5782,7 +5799,6 @@ "TRJ": [ ["traj.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 146, "path": "5e2/0fe/5e20fe22000d94eb54ce0e030c1dd2439796b331/839c970611cedad2e65068b6e412d84c12831ed6/" } @@ -5834,6 +5850,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 429, + "AUTHORS_CONTACT": "Kiirikki, M. Anne; Ollila O. H. Samuli", "path": "2b9/b0d/2b9b0d32b79cea2fe66a283bf52e9c1f648393e4/b9251450aa7886b4109908c1ada3d666a77ba77b/" } }, @@ -5865,7 +5882,7 @@ "NAME": "PC", "MOLTYPE": "system1", "COUNT": [175, 175], - "MAPPING": "mappingPOPClipid17.yaml" + "MAPPING": "mappingPOPC_AmberLipid.yaml" }, "SOL": { "NAME": "SOL", "COUNT": 26265, "MAPPING": "mappingTIP3Pwater.yaml" }, "SOD": { "NAME": "NA", "COUNT": 88, "MAPPING": "mappingSODlipid17.yaml" } @@ -5877,6 +5894,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 50, "DOI": "10.5281/zenodo.3693681", + "AUTHORS_CONTACT": "Virtanen, Salla; Ollila, O.H.Samuli", "TRAJECTORY_SIZE": 4438480544, "TPR": [ ["topol.tpr"] @@ -5884,7 +5902,6 @@ "TRJ": [ ["trajSKIP.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 317, "path": "25a/ce9/25ace931487aad89f9e755125358282fe99d8ea8/7ce1e2a0f5027d28b81cab28c850ef64d5c9aff5/" } diff --git a/Ranking/SYSTEM_tails_Ranking.json b/Ranking/SYSTEM_tails_Ranking.json index 25ad5434f..823b63ce5 100644 --- a/Ranking/SYSTEM_tails_Ranking.json +++ b/Ranking/SYSTEM_tails_Ranking.json @@ -617,7 +617,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [32, 32] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 3200 } @@ -658,6 +658,7 @@ "TotalQuality": { "headgroup": 0.620293, "tails": 0.728064, "total": 0.69214, "FFQuality": 0.455 }, "system": { "DOI": "10.5281/zenodo.166034", + "AUTHORS_CONTACT": "Favela-Rosales, Fernando", "SYSTEM": "POPC_T298K", "SOFTWARE": "gromacs", "FF": "Slipids", @@ -713,7 +714,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [512, 512] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 51200 } @@ -820,7 +821,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [128, 128] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 12800 } @@ -961,6 +962,8 @@ "TotalQuality": { "headgroup": 0.11395, "tails": 0.709066, "total": 0.510694, "FFQuality": 1.555 }, "system": { "DOI": "10.5281/zenodo.14713793", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", + "FF": "Sage 2.2.1", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -974,7 +977,7 @@ "POPC": { "NAME": "POPC", "MAPPING": "mappingPOPCsage_smiles.yaml", - "COUNT": [128, 0] + "COUNT": [64, 64] }, "SOL": { "NAME": "TIP3P", "MAPPING": "mappingTIP3Psage_smiles.yaml", "COUNT": 5120 } }, @@ -982,7 +985,6 @@ "TOP": [ ["bilayer.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 612503984, "TRJLENGTH": 500100, "TEMPERATURE": 300, @@ -2261,6 +2263,7 @@ "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, "ID": 797, + "AUTHORS_CONTACT": "Hoeflich, Julianne", "path": "4f5/fb4/4f5fb4c911390b50b56d06364c85910c10191c57/ea16a8b51b9d71838d911eb3cebbc69ad05600d8/" } }, @@ -2269,6 +2272,7 @@ "TotalQuality": { "headgroup": 0.556067, "tails": 0.567598, "total": 0.563754, "FFQuality": 1.355 }, "system": { "DOI": "10.5281/zenodo.15021844", + "AUTHORS_CONTACT": "Hoeflich, Julianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -2848,6 +2852,7 @@ "TotalQuality": { "headgroup": 0.117569, "tails": 0.44331, "total": 0.334729, "FFQuality": 2.155 }, "system": { "DOI": "10.5281/zenodo.15065748", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -3251,6 +3256,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 430, + "AUTHORS_CONTACT": "Javanainen, Matti", "path": "2d4/61b/2d461bc9d828af155146162ef42438974e4cbeaf/c8ce4cc36ef6ec7a085cf011176a92d9d746a792/" } }, @@ -3419,6 +3425,8 @@ "TotalQuality": { "headgroup": 0.549462, "tails": 0.310135, "total": 0.389911, "FFQuality": 2.355 }, "system": { "DOI": "10.5281/zenodo.14713771", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", + "FF": "Sage 2.2.1", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -3432,7 +3440,7 @@ "POPC": { "NAME": "POPC", "MAPPING": "mappingPOPCsage_smiles.yaml", - "COUNT": [128, 0] + "COUNT": [64, 64] }, "SOL": { "NAME": "TIP3P", "MAPPING": "mappingTIP3Psage_smiles.yaml", "COUNT": 5120 } }, @@ -3505,6 +3513,7 @@ "TRJLENGTH": 300100, "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 558, + "AUTHORS_CONTACT": "Papadopoulos, Chris; Fuchs, Patrick F.J.", "path": "a63/ca7/a63ca7001cbd5cfc328da122668d1aebc00f2c91/220540156a6ac7813942fd01d998a491b6ff9b8b/" } }, @@ -3948,7 +3957,7 @@ "COMPOSITION": { "POPE": { "NAME": "PE", - "MAPPING": "mappingPOPElipid17.yaml", + "MAPPING": "mappingPOPE_AmberLipid.yaml", "COUNT": [250, 250] }, "SOL": { "NAME": "WAT", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 25000 } @@ -4037,6 +4046,7 @@ "TotalQuality": { "headgroup": 0.536115, "tails": 0.199196, "total": 0.311503, "FFQuality": 3.045 }, "system": { "DOI": "10.5281/zenodo.15065566", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -4295,6 +4305,7 @@ "TotalQuality": { "headgroup": 0.529893, "tails": 0.177282, "total": 0.294819, "FFQuality": 1.645 }, "system": { "DOI": "10.5281/zenodo.15002801", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -4319,7 +4330,6 @@ "TOP": [ ["bilayer5.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 414960964, "TRJLENGTH": 338800, "TEMPERATURE": 300, @@ -4341,6 +4351,7 @@ "TotalQuality": { "headgroup": 0.476603, "tails": 0.176768, "total": 0.276713, "FFQuality": 1.845 }, "system": { "DOI": "10.5281/zenodo.15002712", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -4365,7 +4376,6 @@ "TOP": [ ["bilayer2.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 350763692, "TRJLENGTH": 286400, "TEMPERATURE": 300, @@ -5157,6 +5167,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 400, "DOI": "10.5281/zenodo.1129415", + "AUTHORS_CONTACT": "Piggot, Thomas", "TRAJECTORY_SIZE": 221970700, "TPR": [ ["for-md-CHARMM36_POPS_298K_v2.tpr"] @@ -5164,7 +5175,6 @@ "TRJ": [ ["md-CHARMM36_10A-switch_POPS_v2_400-500ns_skip10.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 5, "path": "1b2/6e6/1b26e6c750b4f39c37770422cd4d3c40240cf111/995bc873b811ca09c916b47784fa33bb9d793732/" } @@ -5210,6 +5220,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 106, + "AUTHORS_CONTACT": "Thomas Piggot", "path": "f40/bb6/f40bb6ab5d44402be07059e8df74b5a8200f031e/6774168dfec0a5a7377c8a46341eba603f320cf7/" } }, @@ -5430,6 +5441,7 @@ "TotalQuality": { "headgroup": 0.249069, "tails": 0.0209952, "total": 0.0970196, "FFQuality": 1.677 }, "system": { "DOI": "10.5281/zenodo.10467181", + "AUTHORS_CONTACT": "Nencini, Ricky", "TRJ": [ ["POPS_144_144_Na_contraions_prosECCo75.xtc"] ], @@ -5525,6 +5537,7 @@ }, "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "path": "e2b/09a/e2b09acaead3655073b4ed768e4a08d879b0042d/bb294604ef4b17df4b59195e2ac600630d33c644/" } }, @@ -5571,6 +5584,7 @@ }, "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "path": "58d/654/58d654af9894439448a86b0c7a9f13020d41d54d/afaaae028c976185c3ce34198181af80a226d37f/" } } diff --git a/Ranking/SYSTEM_total_Ranking.json b/Ranking/SYSTEM_total_Ranking.json index 94bff47c3..f645eab1c 100644 --- a/Ranking/SYSTEM_total_Ranking.json +++ b/Ranking/SYSTEM_total_Ranking.json @@ -554,6 +554,7 @@ "TotalQuality": { "headgroup": 0.620293, "tails": 0.728064, "total": 0.69214, "FFQuality": 0.455 }, "system": { "DOI": "10.5281/zenodo.166034", + "AUTHORS_CONTACT": "Favela-Rosales, Fernando", "SYSTEM": "POPC_T298K", "SOFTWARE": "gromacs", "FF": "Slipids", @@ -609,7 +610,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [512, 512] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 51200 } @@ -713,7 +714,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [128, 128] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 12800 } @@ -984,7 +985,7 @@ "COMPOSITION": { "POPC": { "NAME": "PC", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [32, 32] }, "SOL": { "NAME": "TP3", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 3200 } @@ -1702,6 +1703,7 @@ "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, "ID": 797, + "AUTHORS_CONTACT": "Hoeflich, Julianne", "path": "4f5/fb4/4f5fb4c911390b50b56d06364c85910c10191c57/ea16a8b51b9d71838d911eb3cebbc69ad05600d8/" } }, @@ -1804,6 +1806,7 @@ "TotalQuality": { "headgroup": 0.556067, "tails": 0.567598, "total": 0.563754, "FFQuality": 1.355 }, "system": { "DOI": "10.5281/zenodo.15021844", + "AUTHORS_CONTACT": "Hoeflich, Julianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -2322,6 +2325,8 @@ "TotalQuality": { "headgroup": 0.11395, "tails": 0.709066, "total": 0.510694, "FFQuality": 1.555 }, "system": { "DOI": "10.5281/zenodo.14713793", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", + "FF": "Sage 2.2.1", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -2335,7 +2340,7 @@ "POPC": { "NAME": "POPC", "MAPPING": "mappingPOPCsage_smiles.yaml", - "COUNT": [128, 0] + "COUNT": [64, 64] }, "SOL": { "NAME": "TIP3P", "MAPPING": "mappingTIP3Psage_smiles.yaml", "COUNT": 5120 } }, @@ -2343,7 +2348,6 @@ "TOP": [ ["bilayer.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 612503984, "TRJLENGTH": 500100, "TEMPERATURE": 300, @@ -2717,6 +2721,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 430, + "AUTHORS_CONTACT": "Javanainen, Matti", "path": "2d4/61b/2d461bc9d828af155146162ef42438974e4cbeaf/c8ce4cc36ef6ec7a085cf011176a92d9d746a792/" } }, @@ -2822,6 +2827,7 @@ "TRJLENGTH": 300100, "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 558, + "AUTHORS_CONTACT": "Papadopoulos, Chris; Fuchs, Patrick F.J.", "path": "a63/ca7/a63ca7001cbd5cfc328da122668d1aebc00f2c91/220540156a6ac7813942fd01d998a491b6ff9b8b/" } }, @@ -3210,6 +3216,8 @@ "TotalQuality": { "headgroup": 0.549462, "tails": 0.310135, "total": 0.389911, "FFQuality": 2.355 }, "system": { "DOI": "10.5281/zenodo.14713771", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", + "FF": "Sage 2.2.1", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -3223,7 +3231,7 @@ "POPC": { "NAME": "POPC", "MAPPING": "mappingPOPCsage_smiles.yaml", - "COUNT": [128, 0] + "COUNT": [64, 64] }, "SOL": { "NAME": "TIP3P", "MAPPING": "mappingTIP3Psage_smiles.yaml", "COUNT": 5120 } }, @@ -3562,6 +3570,7 @@ "TotalQuality": { "headgroup": 0.117569, "tails": 0.44331, "total": 0.334729, "FFQuality": 2.155 }, "system": { "DOI": "10.5281/zenodo.15065748", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -3710,6 +3719,7 @@ "TotalQuality": { "headgroup": 0.536115, "tails": 0.199196, "total": 0.311503, "FFQuality": 3.045 }, "system": { "DOI": "10.5281/zenodo.15065566", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -3921,6 +3931,7 @@ "TotalQuality": { "headgroup": 0.529893, "tails": 0.177282, "total": 0.294819, "FFQuality": 1.645 }, "system": { "DOI": "10.5281/zenodo.15002801", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -3945,7 +3956,6 @@ "TOP": [ ["bilayer5.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 414960964, "TRJLENGTH": 338800, "TEMPERATURE": 300, @@ -4121,6 +4131,7 @@ "TotalQuality": { "headgroup": 0.476603, "tails": 0.176768, "total": 0.276713, "FFQuality": 1.845 }, "system": { "DOI": "10.5281/zenodo.15002712", + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "TRJ": [ ["md_every_100_ps.xtc"] ], @@ -4145,7 +4156,6 @@ "TOP": [ ["bilayer2.top"] ], - "DIR_WRK": "/media/julianne/DATA/Lipids/NMRLipids/temp/", "TRAJECTORY_SIZE": 350763692, "TRJLENGTH": 286400, "TEMPERATURE": 300, @@ -4500,7 +4510,7 @@ "COMPOSITION": { "POPE": { "NAME": "PE", - "MAPPING": "mappingPOPElipid17.yaml", + "MAPPING": "mappingPOPE_AmberLipid.yaml", "COUNT": [250, 250] }, "SOL": { "NAME": "WAT", "MAPPING": "mappingTIP3Plipid17.yaml", "COUNT": 25000 } @@ -4577,6 +4587,7 @@ }, "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "path": "e2b/09a/e2b09acaead3655073b4ed768e4a08d879b0042d/bb294604ef4b17df4b59195e2ac600630d33c644/" } }, @@ -4929,6 +4940,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 400, "DOI": "10.5281/zenodo.1129415", + "AUTHORS_CONTACT": "Piggot, Thomas", "TRAJECTORY_SIZE": 221970700, "TPR": [ ["for-md-CHARMM36_POPS_298K_v2.tpr"] @@ -4936,7 +4948,6 @@ "TRJ": [ ["md-CHARMM36_10A-switch_POPS_v2_400-500ns_skip10.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 5, "path": "1b2/6e6/1b26e6c750b4f39c37770422cd4d3c40240cf111/995bc873b811ca09c916b47784fa33bb9d793732/" } @@ -5088,6 +5099,7 @@ }, "FORMFACTOR": ["unpublished/NMRlipidsIII/1"] }, + "AUTHORS_CONTACT": "Hoelfich, Jullianne", "path": "58d/654/58d654af9894439448a86b0c7a9f13020d41d54d/afaaae028c976185c3ce34198181af80a226d37f/" } }, @@ -5146,6 +5158,7 @@ "TotalQuality": { "headgroup": 0.249069, "tails": 0.0209952, "total": 0.0970196, "FFQuality": 1.677 }, "system": { "DOI": "10.5281/zenodo.10467181", + "AUTHORS_CONTACT": "Nencini, Ricky", "TRJ": [ ["POPS_144_144_Na_contraions_prosECCo75.xtc"] ], @@ -5239,6 +5252,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 106, + "AUTHORS_CONTACT": "Thomas Piggot", "path": "f40/bb6/f40bb6ab5d44402be07059e8df74b5a8200f031e/6774168dfec0a5a7377c8a46341eba603f320cf7/" } }, @@ -5592,7 +5606,7 @@ "POPC": { "NAME": "PC", "MOLTYPE": "system1", - "MAPPING": "mappingPOPClipid17.yaml", + "MAPPING": "mappingPOPC_AmberLipid.yaml", "COUNT": [76, 74] }, "POPG": { @@ -5681,6 +5695,7 @@ "FORMFACTOR": [] }, "ID": 307, + "AUTHORS_CONTACT": "Javanainen, Matti", "path": "c74/6ca/c746ca52b71d685e53a802e8046e1253baf6af2b/8850a90345eb033df4ae3228c3b9fa1fbbe40162/" } }, @@ -5731,6 +5746,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 58, + "AUTHORS_CONTACT": "Kiirikki, M. Anne; Ollila O. H. Samuli", "path": "be6/5d5/be65d56aa0b9732c1f75b8e2de40133ac6c5f706/fe08222fa3d4cc603161b05233be0af37dd3cc8b/" } }, @@ -5772,6 +5788,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 100, "DOI": "10.5281/zenodo.3997116", + "AUTHORS_CONTACT": "Kiirikki, M. Anne; Ollila, O. H. Samuli", "TRAJECTORY_SIZE": 7413293748, "TPR": [ ["run_400ns.tpr"] @@ -5779,7 +5796,6 @@ "TRJ": [ ["100-400ns.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 592, "path": "0c2/1a9/0c21a9be136ea0eb9df9e5c6cdc19f723a0af245/9ac73b6a98acb54a7a67a5d690794ad7f1e4a1d1/" } @@ -5822,6 +5838,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 0, "DOI": "10.5281/zenodo.3859339", + "AUTHORS_CONTACT": "Ollila, O.H.Samuli; Virtanen, I.Salla", "TRAJECTORY_SIZE": 8278576984, "TPR": [ ["topol.tpr"] @@ -5829,7 +5846,6 @@ "TRJ": [ ["traj.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 146, "path": "5e2/0fe/5e20fe22000d94eb54ce0e030c1dd2439796b331/839c970611cedad2e65068b6e412d84c12831ed6/" } @@ -5881,6 +5897,7 @@ ], "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 429, + "AUTHORS_CONTACT": "Kiirikki, M. Anne; Ollila O. H. Samuli", "path": "2b9/b0d/2b9b0d32b79cea2fe66a283bf52e9c1f648393e4/b9251450aa7886b4109908c1ada3d666a77ba77b/" } }, @@ -5912,7 +5929,7 @@ "NAME": "PC", "MOLTYPE": "system1", "COUNT": [175, 175], - "MAPPING": "mappingPOPClipid17.yaml" + "MAPPING": "mappingPOPC_AmberLipid.yaml" }, "SOL": { "NAME": "SOL", "COUNT": 26265, "MAPPING": "mappingTIP3Pwater.yaml" }, "SOD": { "NAME": "NA", "COUNT": 88, "MAPPING": "mappingSODlipid17.yaml" } @@ -5924,6 +5941,7 @@ "SOFTWARE": "gromacs", "PREEQTIME": 50, "DOI": "10.5281/zenodo.3693681", + "AUTHORS_CONTACT": "Virtanen, Salla; Ollila, O.H.Samuli", "TRAJECTORY_SIZE": 4438480544, "TPR": [ ["topol.tpr"] @@ -5931,7 +5949,6 @@ "TRJ": [ ["trajSKIP.xtc"] ], - "DIR_WRK": "/media/osollila/Data/tmp/DATABANK/", "ID": 317, "path": "25a/ce9/25ace931487aad89f9e755125358282fe99d8ea8/7ce1e2a0f5027d28b81cab28c850ef64d5c9aff5/" } diff --git a/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/POPC_OrderParameters_quality.json b/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/POPC_OrderParameters_quality.json new file mode 100644 index 000000000..9e26dfeeb --- /dev/null +++ b/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/POPC_OrderParameters_quality.json @@ -0,0 +1 @@ +{} \ No newline at end of file diff --git a/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/README.yaml b/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/README.yaml index d58fbc9ef..1601f7510 100644 --- a/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/README.yaml +++ b/Simulations/1d0/5fe/1d05fe97e0d99fc700ba25dd4f28b8f75758fb3a/9743c5e991c6a9291162166e57dff7183f6a3dcf/README.yaml @@ -42,4 +42,8 @@ TRJLENGTH: 899730.0 NUMBER_OF_ATOMS: 53600 DATEOFRUNNING: 06/01/2026 TYPEOFSYSTEM: lipid bilayer +EXPERIMENT: + ORDERPARAMETER: + POPC: [] + FORMFACTOR: [] ID: 869 diff --git a/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/POPC_OrderParameters_quality.json b/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/POPC_OrderParameters_quality.json new file mode 100644 index 000000000..9e26dfeeb --- /dev/null +++ b/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/POPC_OrderParameters_quality.json @@ -0,0 +1 @@ +{} \ No newline at end of file diff --git a/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/README.yaml b/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/README.yaml index fff721501..a1470728a 100644 --- a/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/README.yaml +++ b/Simulations/347/ae8/347ae8a9b0e8351a27c87337326ecfad6bc623cf/345e7a2be94a2692fec298aeccc31e44b29c38d3/README.yaml @@ -42,4 +42,8 @@ TRJLENGTH: 899610.0 NUMBER_OF_ATOMS: 53760 DATEOFRUNNING: 06/01/2026 TYPEOFSYSTEM: lipid bilayer +EXPERIMENT: + ORDERPARAMETER: + POPC: [] + FORMFACTOR: [] ID: 871 diff --git a/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/POPC_OrderParameters_quality.json b/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/POPC_OrderParameters_quality.json new file mode 100644 index 000000000..9e26dfeeb --- /dev/null +++ b/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/POPC_OrderParameters_quality.json @@ -0,0 +1 @@ +{} \ No newline at end of file diff --git a/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/POPI_OrderParameters_quality.json b/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/POPI_OrderParameters_quality.json new file mode 100644 index 000000000..9e26dfeeb --- /dev/null +++ b/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/POPI_OrderParameters_quality.json @@ -0,0 +1 @@ +{} \ No newline at end of file diff --git a/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/README.yaml b/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/README.yaml index ba1c37f2b..32915d50a 100644 --- a/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/README.yaml +++ b/Simulations/a7e/178/a7e1783cd2c8124d8f0acf0b35700ec2596ff889/fbb2bece23092fce438a7a236b421af208f287eb/README.yaml @@ -47,4 +47,9 @@ TRJLENGTH: 500010.0 NUMBER_OF_ATOMS: 58080 DATEOFRUNNING: 05/01/2026 TYPEOFSYSTEM: lipid bilayer +EXPERIMENT: + ORDERPARAMETER: + POPI: [] + POPC: [] + FORMFACTOR: [] ID: 870 diff --git a/Simulations/c04/cdb/c04cdb61143bb72ba2ddee11599e6bbfaf6cb211/a31f42800216d84d2242eae2af8ac2cbd6b033ee/README.yaml b/Simulations/c04/cdb/c04cdb61143bb72ba2ddee11599e6bbfaf6cb211/a31f42800216d84d2242eae2af8ac2cbd6b033ee/README.yaml index 7ad408108..f151c830b 100644 --- a/Simulations/c04/cdb/c04cdb61143bb72ba2ddee11599e6bbfaf6cb211/a31f42800216d84d2242eae2af8ac2cbd6b033ee/README.yaml +++ b/Simulations/c04/cdb/c04cdb61143bb72ba2ddee11599e6bbfaf6cb211/a31f42800216d84d2242eae2af8ac2cbd6b033ee/README.yaml @@ -1,6 +1,6 @@ DOI: 10.5281/zenodo.14713793 AUTHORS_CONTACT: Hoelfich, Jullianne -FF: Sage 2.2.1 +FF: Sage 2.2.1 TRJ: - - md_every_100_ps.xtc TPR: