Merge pull request #5 from NMRLipids/main

Quality evalution merged to main branch now
NMRLipids · Nov 2, 2021 · c3964b3 · c3964b3
2 parents 590777c + 9915bca
commit c3964b3
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Showing 309 changed files with 9,378 additions and 6,773 deletions.
diff --git a/...2145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/CHOL_OrderParameters_quality.json b/...2145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/CHOL_OrderParameters_quality.json
diff --git a/...2145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/POPC_OrderParameters_quality.json b/...2145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/POPC_OrderParameters_quality.json
diff --git a/...59139e730fc43b244726992145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/README.yaml b/...59139e730fc43b244726992145c2f37a1461/3c99810c45a83b4ba0e54a69fdea8817498a8930/README.yaml
@@ -1,47 +1,47 @@
-DOI: 10.5281/zenodo.3237420
-SOFTWARE: gromacs
-TRJ:
-- - chol10_500ns.xtc
-TPR:
-- - chol10.tpr
-PREEQTIME: 0
-TIMELEFTOUT: 0
-DIR_WRK: /media/osollila/Data/tmp/DATABANK/
-PUBLICATION: null
 AUTHORS_CONTACT: Javanainen, Matti
+FF_DATE: null
 SYSTEM: 22CHOL_200POPC_9000SOL_310K
-SOFTWARE_VERSION: 5.0
-FF: CHARMM36
+TYPEOFSYSTEM: lipid bilayer
+TEMPERATURE: 310.15
+PUBLICATION: null
+NUMBER_OF_ATOMS: 55428
+EXPERIMENT:
+  CHOL: {}
+  POPC: {}
 FF_SOURCE: CHARMM-GUI
-FF_DATE: null
-CPT:
-- - chol10_500ns.cpt
-LOG: null
-TOP:
-- - chol10.top
 COMPOSITION:
   CHOL:
     NAME: CHL1
-    MAPPING: mappingCHOLESTEROLcharmm.txt
     COUNT:
     - 10
     - 12
+    MAPPING: mappingCHOLESTEROLcharmm.txt
   POPC:
     NAME: POPC
-    MAPPING: mappingPOPCcharmm.txt
     COUNT:
     - 100
     - 100
+    MAPPING: mappingPOPCcharmm.txt
   SOL:
     NAME: TIP3
-    MAPPING: mappingTIP3PCHARMMgui.txt
     COUNT: 9000
-TRAJECTORY_SIZE: 1025713704
+    MAPPING: mappingTIP3PCHARMMgui.txt
+TIMELEFTOUT: 0
+CPT:
+- - chol10_500ns.cpt
 TRJLENGTH: 500100.0
-TEMPERATURE: 310.15
-NUMBER_OF_ATOMS: 55428
+TRAJECTORY_SIZE: 1025713704
+SOFTWARE_VERSION: 5.0
+FF: CHARMM36
+TOP:
+- - chol10.top
+PREEQTIME: 0
+DOI: 10.5281/zenodo.3237420
 DATEOFRUNNING: 05/10/2021
-TYPEOFSYSTEM: lipid bilayer
-EXPERIMENT:
-  CHOL: {}
-  POPC: {}
+TPR:
+- - chol10.tpr
+TRJ:
+- - chol10_500ns.xtc
+LOG: null
+SOFTWARE: gromacs
+DIR_WRK: /media/osollila/Data/tmp/DATABANK/
diff --git a/...94777cfaf4a3bbaf66335df4b9aa48c990e0/542f342c6c9c1b0647bcb98de53be96d5af4b505/README.yaml b/...94777cfaf4a3bbaf66335df4b9aa48c990e0/542f342c6c9c1b0647bcb98de53be96d5af4b505/README.yaml
@@ -1,47 +1,47 @@
-DOI: 10.5281/zenodo.35193
-SOFTWARE: gromacs
-TRJ:
-- - 500.xtc
-TPR:
-- - 500.tpr
-PREEQTIME: 0
-TIMELEFTOUT: 0
-DIR_WRK: /usr/home/bort/Databank
-PUBLICATION: null
 AUTHORS_CONTACT: Javanainen, Matti
+FF_DATE: pre-2020
 SYSTEM: 200POPC_9000SOL_81SOD_81CLA_310K
-SOFTWARE_VERSION: 4.6
-FF: Slipids for lipids, Kohagen for NaCl
+TYPEOFSYSTEM: lipid bilayer
+TEMPERATURE: 310.0
+PUBLICATION: null
+NUMBER_OF_ATOMS: 53962
+EXPERIMENT:
+  POPC: {}
 FF_SOURCE: http://mmkluster.fos.su.se/slipids/ and https://bitbucket.org/hseara/ions/
-FF_DATE: pre-2020
-CPT: null
-LOG: null
-TOP:
-- - 500.top
 COMPOSITION:
+  CLA:
+    NAME: CL
+    COUNT: 81
+    MAPPING: mappingCL.txt
   POPC:
     NAME: POPC
-    MAPPING: mappingPOPCslipids.txt
     COUNT:
     - 100
     - 100
+    MAPPING: mappingPOPCslipids.txt
   SOL:
     NAME: SOL
-    MAPPING: mappingTIP3PwaterSlipids.txt
     COUNT: 9000
+    MAPPING: mappingTIP3PwaterSlipids.txt
   SOD:
     NAME: NA
-    MAPPING: mappingNA.txt
-    COUNT: 81
-  CLA:
-    NAME: CL
-    MAPPING: mappingCL.txt
     COUNT: 81
-TRAJECTORY_SIZE: 199059704
+    MAPPING: mappingNA.txt
+TIMELEFTOUT: 0
+CPT: null
 TRJLENGTH: 100100.0
-TEMPERATURE: 310.0
-NUMBER_OF_ATOMS: 53962
+TRAJECTORY_SIZE: 199059704
+SOFTWARE_VERSION: 4.6
+FF: Slipids for lipids, Kohagen for NaCl
+TOP:
+- - 500.top
+PREEQTIME: 0
+DOI: 10.5281/zenodo.35193
 DATEOFRUNNING: 12/10/2021
-TYPEOFSYSTEM: lipid bilayer
-EXPERIMENT:
-  POPC: {}
+TPR:
+- - 500.tpr
+TRJ:
+- - 500.xtc
+LOG: null
+SOFTWARE: gromacs
+DIR_WRK: /usr/home/bort/Databank
diff --git a/...d172073ee268b07f29ecd413eb9de13a3d47/895cd634e9106b949e0c15cd8873592748b66fed/README.yaml b/...d172073ee268b07f29ecd413eb9de13a3d47/895cd634e9106b949e0c15cd8873592748b66fed/README.yaml
@@ -1,41 +1,41 @@
-DOI: 10.5281/zenodo.4040423
-SOFTWARE: gromacs
-TRJ:
-- - run.xtc
-TPR:
-- - run.tpr
-PREEQTIME: 0
-TIMELEFTOUT: 20
-DIR_WRK: /media/osollila/Data/tmp/DATABANK/
-PUBLICATION: null
 AUTHORS_CONTACT: Ollila
+FF_DATE: null
 SYSTEM: 200POPC_9000SOL_313K
-SOFTWARE_VERSION: 5
-FF: CHARMM36
+TYPEOFSYSTEM: lipid bilayer
+TEMPERATURE: 313.0
+PUBLICATION: null
+NUMBER_OF_ATOMS: 53800
+EXPERIMENT:
+  POPC: {}
 FF_SOURCE: null
-FF_DATE: null
-CPT:
-- - run.cpt
-LOG:
-- - run.log
-TOP:
-- - topol.top
 COMPOSITION:
   POPC:
     NAME: POPC
-    MAPPING: mappingPOPCcharmm.txt
     COUNT:
     - 100
     - 100
+    MAPPING: mappingPOPCcharmm.txt
   SOL:
     NAME: TIP3
-    MAPPING: mappingTIP3PCHARMMgui.txt
     COUNT: 9000
-TRAJECTORY_SIZE: 3979765856
+    MAPPING: mappingTIP3PCHARMMgui.txt
+TIMELEFTOUT: 20
+CPT:
+- - run.cpt
 TRJLENGTH: 200010.0
-TEMPERATURE: 313.0
-NUMBER_OF_ATOMS: 53800
+TRAJECTORY_SIZE: 3979765856
+SOFTWARE_VERSION: 5
+FF: CHARMM36
+TOP:
+- - topol.top
+PREEQTIME: 0
+DOI: 10.5281/zenodo.4040423
 DATEOFRUNNING: 01/10/2021
-TYPEOFSYSTEM: lipid bilayer
-EXPERIMENT:
-  POPC: {}
+TPR:
+- - run.tpr
+TRJ:
+- - run.xtc
+LOG:
+- - run.log
+SOFTWARE: gromacs
+DIR_WRK: /media/osollila/Data/tmp/DATABANK/
diff --git a/...943ecae9627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/POPS_FragmentQuality.json b/...943ecae9627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/POPS_FragmentQuality.json
@@ -1 +1 @@
-{"10.1021/acs.jctc.9b00824": {"headgroup": "nan", "sn-1": 0.387035064985739, "sn-2": 0.40672910944370105}, "10.1021/acs.jpcb.9b06091": {"headgroup": 1.0965931627454113, "sn-1": "nan", "sn-2": "nan"}}
+{"10.1021/acs.jctc.9b00824": {"headgroup": "nan", "sn-1": 8.981029995245864, "sn-2": 8.384774565237057}, "10.1021/acs.jpcb.9b06091": {"headgroup": 171.44264853135417, "sn-1": "nan", "sn-2": "nan"}}
diff --git a/...627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/POPS_OrderParameters_quality.json b/...627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/POPS_OrderParameters_quality.json
diff --git a/...8418d9965749ac943ecae9627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/README.yaml b/...8418d9965749ac943ecae9627cfdd1dfbdcd/7339faa76da6c93cfee03e59f399e2eed1628b53/README.yaml
@@ -1,44 +1,44 @@
-DOI: 10.5281/zenodo.1129441
-SOFTWARE: gromacs
-TRJ:
-- - md-Slipids_LJ-PME_POPS_v2_400-500ns_skip10.xtc
-TPR:
-- - for-md-Slipids_10A_cut-off_LJ-PME_POPS_298K_v2.tpr
-PREEQTIME: 400
-TIMELEFTOUT: 0
-DIR_WRK: /usr/home/bort/Databank
-PUBLICATION: null
 AUTHORS_CONTACT: Thomas Piggot
+FF_DATE: pre-2020
 SYSTEM: 128POPS_4880SOL_128SOD_298K_v2
-SOFTWARE_VERSION: null
-FF: Slipids
+TYPEOFSYSTEM: lipid bilayer
+TEMPERATURE: 298.0
+PUBLICATION: null
+NUMBER_OF_ATOMS: 29824
+EXPERIMENT:
+  POPS:
+    10.1021/acs.jctc.9b00824: 10.1021/acs.jctc.9b00824/1
+    10.1021/acs.jpcb.9b06091: 10.1021/acs.jpcb.9b06091/1
 FF_SOURCE: starting structure from CHARMM-GUI
-FF_DATE: pre-2020
-CPT: null
-LOG: null
-TOP: null
 COMPOSITION:
   POPS:
     NAME: POPS
-    MAPPING: mappingPOPSslipids.txt
     COUNT:
     - 64
     - 64
+    MAPPING: mappingPOPSslipids.txt
   SOL:
     NAME: SOL
-    MAPPING: mappingSPCwater.txt
     COUNT: 4480
+    MAPPING: mappingSPCwater.txt
   SOD:
     NAME: NA
-    MAPPING: mappingNA.txt
     COUNT: 128
-TRAJECTORY_SIZE: 221910896
+    MAPPING: mappingNA.txt
+TIMELEFTOUT: 0
+CPT: null
 TRJLENGTH: 100050.0
-TEMPERATURE: 298.0
-NUMBER_OF_ATOMS: 29824
+TRAJECTORY_SIZE: 221910896
+SOFTWARE_VERSION: null
+FF: Slipids
+TOP: null
+PREEQTIME: 400
+DOI: 10.5281/zenodo.1129441
 DATEOFRUNNING: 12/10/2021
-TYPEOFSYSTEM: lipid bilayer
-EXPERIMENT:
-  POPS:
-    10.1021/acs.jctc.9b00824: 10.1021/acs.jctc.9b00824/1
-    10.1021/acs.jpcb.9b06091: 10.1021/acs.jpcb.9b06091/1
+TPR:
+- - for-md-Slipids_10A_cut-off_LJ-PME_POPS_298K_v2.tpr
+TRJ:
+- - md-Slipids_LJ-PME_POPS_v2_400-500ns_skip10.xtc
+LOG: null
+SOFTWARE: gromacs
+DIR_WRK: /usr/home/bort/Databank
diff --git a/...220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml b/...220d27c2d6f4aa76992ae66014ac8d5557e0/4237bd2c8e11c1b48325386fd672fd6fd3e75894/README.yaml
@@ -1,48 +1,48 @@
-DOI: 10.5281/zenodo.45008
-SOFTWARE: gromacs
-TRJ:
-- - md.xtc
-TPR:
-- - md.tpr
-PREEQTIME: 700
-TIMELEFTOUT: 0
-DIR_WRK: /usr/home/bort/Databank
-PUBLICATION: null
 AUTHORS_CONTACT: Javanainen, Matti
+FF_DATE: null
 SYSTEM: 200POPC_9000SOL_73CAL_146CLA_310K
-SOFTWARE_VERSION: 5.0
-FF: CHARMM36 with ECC-scaled ions
+TYPEOFSYSTEM: lipid bilayer
+TEMPERATURE: 310.15
+PUBLICATION: null
+NUMBER_OF_ATOMS: 54019
+EXPERIMENT:
+  POPC: {}
 FF_SOURCE: http://www.charmm-gui.org for lipids and https://bitbucket.org/hseara/ions/
   for ions
-FF_DATE: null
-CPT: null
-LOG: null
-TOP:
-- - topol.top
 COMPOSITION:
+  SOL:
+    NAME: TIP3
+    COUNT: 9000
+    MAPPING: mappingTIP3PCHARMMgui.txt
   POPC:
     NAME: POPC
-    MAPPING: mappingPOPCcharmm.txt
     COUNT:
     - 100
     - 100
-  SOL:
-    NAME: TIP3
-    MAPPING: mappingTIP3PCHARMMgui.txt
-    COUNT: 9000
+    MAPPING: mappingPOPCcharmm.txt
   CAL:
     NAME: CA
-    MAPPING: mappingCA.txt
     COUNT: 73
+    MAPPING: mappingCA.txt
   CLA:
     NAME: CL
-    MAPPING: mappingCL.txt
     COUNT: 146
-TRAJECTORY_SIZE: 200283872
+    MAPPING: mappingCL.txt
+TIMELEFTOUT: 0
+CPT: null
 TRJLENGTH: 100100.0
-TEMPERATURE: 310.15
-NUMBER_OF_ATOMS: 54019
+TRAJECTORY_SIZE: 200283872
+SOFTWARE_VERSION: 5.0
+FF: CHARMM36 with ECC-scaled ions
+TOP:
+- - topol.top
+PREEQTIME: 700
+DOI: 10.5281/zenodo.45008
 DATEOFRUNNING: 12/10/2021
-TYPEOFSYSTEM: lipid bilayer
-EXPERIMENT:
-  POPC: {}
+TPR:
+- - md.tpr
+TRJ:
+- - md.xtc
+LOG: null
+SOFTWARE: gromacs
+DIR_WRK: /usr/home/bort/Databank