NMRLipids · comcon1 · Jan 12, 2026 · Jan 10, 2026 · Jan 10, 2026 · Jan 10, 2026
diff --git a/...12bed812cc77b3a749ee330cd740ab78eeef/051412bed812cc77b3a749ee330cd740ab78eeef/README.yaml b/...12bed812cc77b3a749ee330cd740ab78eeef/051412bed812cc77b3a749ee330cd740ab78eeef/README.yaml
@@ -24,7 +24,6 @@ COMPOSITION:
     NAME: TIP3
     MAPPING: mappingTIP3PCHARMMgui.yaml
     COUNT: 7200
-DIR_WRK: /media/osollila/Data1/tmp/DATABANK/
 PUBLICATION: null
 AUTHORS_CONTACT: Melcr, Josef
 SYSTEM: 80POPC_80CHOL_7200SOL_303K
@@ -34,7 +33,7 @@ FF_SOURCE: starting structure from CHARMM-GUI Membrane Builder v1.7 (http://www.
 FF_DATE: null
 CHK:
 - - step8_1.chk
-TOP:
+PSF:
 - - step5_charmm2omm.psf
 CRD:
 - - step5_charmm2omm.crd

diff --git a/...06a9172359ef0e7599536966edff86498b63/1c2f06a9172359ef0e7599536966edff86498b63/README.yaml b/...06a9172359ef0e7599536966edff86498b63/1c2f06a9172359ef0e7599536966edff86498b63/README.yaml
@@ -2,8 +2,10 @@ DOI: 10.5281/zenodo.8000065
 SOFTWARE: openMM
 TRJ:
 - - traj.xtc
-PDB:
+PSF:
 - - step2_drude.psf
+PDB:
+- - step2_drude.pdb
 PREEQTIME: 200
 TIMELEFTOUT: 0
 TEMPERATURE: 303
@@ -26,14 +28,13 @@ COMPOSITION:
     NAME: CLA
     MAPPING: mappingCLAcharmmPolarizable.yaml
     COUNT: 82
-DIR_WRK: /home/peptid/drude
 PUBLICATION: null
 AUTHORS_CONTACT: Kav, Batuhan
 SYSTEM: POPC_350_CaCl2_CHARMMdrude2023_303K
 SOFTWARE_VERSION: null
-FF: Charmm-Drude polarizable2023
+FF: Charmm-Drude polarizable
 FF_SOURCE: https://doi.org/10.1021/acs.jctc.3c00203
-FF_DATE: null
+FF_DATE: 2023
 CHK: null
 TOP: null
 CRD: null

diff --git a/...7da411113327d1c0e43eea10b0f096031d45/35a315cecf0156381237417893bf6755b08ab3e8/README.yaml b/...7da411113327d1c0e43eea10b0f096031d45/35a315cecf0156381237417893bf6755b08ab3e8/README.yaml
@@ -9,14 +9,12 @@ TIMELEFTOUT: 0
 COMPOSITION:
   POPC:
     NAME: PC
-    MOLTYPE: system1
     MAPPING: mappingPOPC_AmberLipid.yaml
     COUNT:
     - 175
     - 175
   POPG:
     NAME: PGR
-    MOLTYPE: system2
     MAPPING: mappingPOPGlipid17.yaml
     COUNT:
     - 44

diff --git a/...95a2fbe4eb6dc3442672820449a667b6c809/fa35f5627cf4ebe0a9d248fc0ff3b5d474181b8c/README.yaml b/...95a2fbe4eb6dc3442672820449a667b6c809/fa35f5627cf4ebe0a9d248fc0ff3b5d474181b8c/README.yaml
@@ -9,14 +9,12 @@ TIMELEFTOUT: 0
 COMPOSITION:
   POPC:
     NAME: PC
-    MOLTYPE: system1
     MAPPING: mappingPOPC_AmberLipid.yaml
     COUNT:
     - 75
     - 75
   POPG:
     NAME: PGR
-    MOLTYPE: system2
     MAPPING: mappingPOPGlipid17.yaml
     COUNT:
     - 76

diff --git a/...257dc453a389dfecaf1774e46253c23f4f5d/21e0257dc453a389dfecaf1774e46253c23f4f5d/README.yaml b/...257dc453a389dfecaf1774e46253c23f4f5d/21e0257dc453a389dfecaf1774e46253c23f4f5d/README.yaml
@@ -2,7 +2,7 @@ DOI: 10.5281/zenodo.7992137
 SOFTWARE: openMM
 TRJ:
 - - traj.dcd
-PDB:
+PSF:
 - - step2_drude.psf
 PREEQTIME: 200
 TIMELEFTOUT: 0

diff --git a/...7f8f740c4466d91660c34cb1c2295265ede5/24497f8f740c4466d91660c34cb1c2295265ede5/README.yaml b/...7f8f740c4466d91660c34cb1c2295265ede5/24497f8f740c4466d91660c34cb1c2295265ede5/README.yaml
@@ -2,7 +2,7 @@ DOI: 10.5281/zenodo.7916287
 SOFTWARE: openMM
 TRJ:
 - - popc1ns.xtc
-PDB:
+PSF:
 - - popc72_drude.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0
@@ -18,14 +18,13 @@ COMPOSITION:
     NAME: SWM4
     MAPPING: mappingSWM4water.yaml
     COUNT: 2239
-DIR_WRK: /home/sosamuli/temp/DataBank/
 PUBLICATION: null
 AUTHORS_CONTACT: Kav, Batuhan
 SYSTEM: POPC_CHARMMdrude2023_303K
 SOFTWARE_VERSION: null
-FF: Charmm-Drude polarizable2023
+FF: Charmm-Drude polarizable
 FF_SOURCE: null
-FF_DATE: null
+FF_DATE: 2023
 CHK: null
 TOP: null
 CRD: null

diff --git a/...e931487aad89f9e755125358282fe99d8ea8/7ce1e2a0f5027d28b81cab28c850ef64d5c9aff5/README.yaml b/...e931487aad89f9e755125358282fe99d8ea8/7ce1e2a0f5027d28b81cab28c850ef64d5c9aff5/README.yaml
@@ -13,14 +13,12 @@ FF_SOURCE: 10.5281/zenodo.2585523
 COMPOSITION:
   POPG:
     NAME: PGR
-    MOLTYPE: system2
     COUNT:
     - 44
     - 44
     MAPPING: mappingPOPGlipid17.yaml
   POPC:
     NAME: PC
-    MOLTYPE: system1
     COUNT:
     - 175
     - 175

diff --git a/...ca556626ecfe2e8c9dbad5cc8b45cdf2c94b/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/README.yaml b/...ca556626ecfe2e8c9dbad5cc8b45cdf2c94b/273eca556626ecfe2e8c9dbad5cc8b45cdf2c94b/README.yaml
@@ -2,7 +2,7 @@ DOI: 10.5281/zenodo.8000095
 SOFTWARE: openMM
 TRJ:
 - - traj.xtc
-PDB:
+PSF:
 - - step2_drude.psf
 PREEQTIME: 200
 TIMELEFTOUT: 0

diff --git a/...e0da10ae3325d69b59feef3a2249b299a706/9789f36a4d076909e29a14c8cc702b794e358691/README.yaml b/...e0da10ae3325d69b59feef3a2249b299a706/9789f36a4d076909e29a14c8cc702b794e358691/README.yaml
@@ -9,14 +9,12 @@ TIMELEFTOUT: 0
 COMPOSITION:
   POPE:
     NAME: PE
-    MOLTYPE: system1
     MAPPING: mappingPOPE_AmberLipid.yaml
     COUNT:
     - 187
     - 187
   POPG:
     NAME: PGR
-    MOLTYPE: system2
     MAPPING: mappingPOPGlipid17.yaml
     COUNT:
     - 63

diff --git a/...69e592b5cb04f2139c462da1fd7814832acd/4416de72d1d15b560aef6adf7222ea774c90b53f/README.yaml b/...69e592b5cb04f2139c462da1fd7814832acd/4416de72d1d15b560aef6adf7222ea774c90b53f/README.yaml
@@ -9,14 +9,12 @@ TIMELEFTOUT: 0
 COMPOSITION:
   POPC:
     NAME: PC
-    MOLTYPE: system1
     MAPPING: mappingPOPC_AmberLipid.yaml
     COUNT:
     - 76
     - 74
   POPG:
     NAME: PGR
-    MOLTYPE: system2
     MAPPING: mappingPOPGlipid17.yaml
     COUNT:
     - 75

diff --git a/...c72e84f8a1d8895cf012fd0ba5e2dbb218f0/e689bf23a1b93998fb38f215c26871379a05247a/README.yaml b/...c72e84f8a1d8895cf012fd0ba5e2dbb218f0/e689bf23a1b93998fb38f215c26871379a05247a/README.yaml
@@ -9,14 +9,12 @@ TIMELEFTOUT: 0
 COMPOSITION:
   POPE:
     NAME: PE
-    MOLTYPE: system1
     MAPPING: mappingPOPE_AmberLipid.yaml
     COUNT:
     - 187
     - 187
   POPG:
     NAME: PGR
-    MOLTYPE: system2
     MAPPING: mappingPOPGlipid17.yaml
     COUNT:
     - 63

diff --git a/...6b17c45fed32bf63492301f79167dda0cc8b/5e076b17c45fed32bf63492301f79167dda0cc8b/README.yaml b/...6b17c45fed32bf63492301f79167dda0cc8b/5e076b17c45fed32bf63492301f79167dda0cc8b/README.yaml
@@ -4,6 +4,8 @@ TRJ:
 - - traj_center.dcd
 PDB:
 - - struct.pdb
+PSF:
+- - struct.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0
 TEMPERATURE: 298
@@ -32,7 +34,6 @@ COMPOSITION:
     NAME: CLA
     MAPPING: mappingCLA.yaml
     COUNT: 35
-DIR_WRK: /home/sosamuli/temp/DataBank/
 PUBLICATION: Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a)
 AUTHORS_CONTACT: Milka Doktorova
 SYSTEM: POPC/PSM (70/30) NAMD

diff --git a/...9e96aca23aeaa4ea2567e0e0cb8b8903a694/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/README.yaml b/...9e96aca23aeaa4ea2567e0e0cb8b8903a694/68d39e96aca23aeaa4ea2567e0e0cb8b8903a694/README.yaml
@@ -4,6 +4,8 @@ TRJ:
 - - traj_center.dcd
 PDB:
 - - struct.pdb
+PSF:
+- - struct.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0
 TEMPERATURE: 328.15
@@ -18,7 +20,6 @@ COMPOSITION:
     NAME: TIP3
     MAPPING: mappingTIP3PCHARMMgui.yaml
     COUNT: 9000
-DIR_WRK: /home/sosamuli/temp/DataBank/
 PUBLICATION: Doktorova et al. 2020 J. Phys. Chem. B. article (DOI 10.1021/acs.jpcb.0c03389)
 AUTHORS_CONTACT: Milka Doktorova
 SYSTEM: PSM NAMD

diff --git a/...bc478e03fca6d1567f3d9451cfe5c8aadc72/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/README.yaml b/...bc478e03fca6d1567f3d9451cfe5c8aadc72/6a1bbc478e03fca6d1567f3d9451cfe5c8aadc72/README.yaml
@@ -2,7 +2,7 @@ DOI: 10.5281/zenodo.7916494
 SOFTWARE: openMM
 TRJ:
 - - pope2ns.xtc
-PDB:
+PSF:
 - - pope72_drude.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0

diff --git a/...a166a012ce72b5552c6cb9589033d9fd3edf/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/README.yaml b/...a166a012ce72b5552c6cb9589033d9fd3edf/6d9ea166a012ce72b5552c6cb9589033d9fd3edf/README.yaml
@@ -4,6 +4,8 @@ TRJ:
 - - traj_center.dcd
 PDB:
 - - struct.pdb
+PDB:
+- - struct.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0
 TEMPERATURE: 303

diff --git a/...3763c456a6837a6d65f48cc7e7b14e4a3a6e/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/README.yaml b/...3763c456a6837a6d65f48cc7e7b14e4a3a6e/780d3763c456a6837a6d65f48cc7e7b14e4a3a6e/README.yaml
@@ -2,7 +2,7 @@ DOI: 10.5281/zenodo.7916287
 SOFTWARE: openMM
 TRJ:
 - - popc3ns.xtc
-PDB:
+PSF:
 - - popc72_drude.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0
@@ -18,7 +18,6 @@ COMPOSITION:
     NAME: SWM4
     MAPPING: mappingSWM4water.yaml
     COUNT: 2239
-DIR_WRK: /home/sosamuli/temp/DataBank/
 PUBLICATION: null
 AUTHORS_CONTACT: Kav, Batuhan
 SYSTEM: POPC_CHARMMdrude2023_303K

diff --git a/...dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml b/...dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml
@@ -4,10 +4,11 @@ TRJ:
 - - ER-like.dcd
 PDB:
 - - ER-like.pdb
+PSF:
+- - ER-like.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0
 TEMPERATURE: 310
-DIR_WRK: /home/sosamuli/temp/DataBank/
 PUBLICATION: null
 AUTHORS_CONTACT: Reza Talandashti and Nathalie Reuter
 SYSTEM: 12CHOL,134POPC,60POPE,14POPS,26POPI,10CER180,10551SOL,40SOD

diff --git a/...101895eed0e5b5344166106a5710ce18a82c/7f1f101895eed0e5b5344166106a5710ce18a82c/README.yaml b/...101895eed0e5b5344166106a5710ce18a82c/7f1f101895eed0e5b5344166106a5710ce18a82c/README.yaml
@@ -2,7 +2,7 @@ DOI: 10.5281/zenodo.7916494
 SOFTWARE: openMM
 TRJ:
 - - pope1ns.xtc
-PDB:
+PSF:
 - - pope72_drude.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0

diff --git a/...1c6616d7eb421861bf4edce710e1fc960984/582a7ab9fa1f0aa9de70eb9d36bc47a52db720b0/README.yaml b/...1c6616d7eb421861bf4edce710e1fc960984/582a7ab9fa1f0aa9de70eb9d36bc47a52db720b0/README.yaml
@@ -9,26 +9,22 @@ TIMELEFTOUT: 0
 COMPOSITION:
   POPG:
     NAME: PGR
-    MOLTYPE: system1
     MAPPING: mappingPOPGlipid17.yaml
     COUNT:
     - 187
     - 187
   POPE:
     NAME: PE
-    MOLTYPE: system2
     MAPPING: mappingPOPE_AmberLipid.yaml
     COUNT:
     - 63
     - 63
   SOD:
     NAME: Na+
-    MOLTYPE: Na+
     MAPPING: mappingNA+.yaml
     COUNT: 374
   SOL:
     NAME: WAT
-    MOLTYPE: WAT
     MAPPING: mappingTIP3Plipid17.yaml
     COUNT: 25000
 DIR_WRK: /usr/home/bort/Databank

diff --git a/...54e9ba7fc98d12d7bebfcc0e9defe3617bd7/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/README.yaml b/...54e9ba7fc98d12d7bebfcc0e9defe3617bd7/9da554e9ba7fc98d12d7bebfcc0e9defe3617bd7/README.yaml
@@ -4,6 +4,8 @@ TRJ:
 - - traj_center_245ns.dcd
 PDB:
 - - struct.pdb
+PDB:
+- - struct.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0
 TEMPERATURE: 298
@@ -18,7 +20,6 @@ COMPOSITION:
     NAME: TIP3
     MAPPING: mappingTIP3PCHARMMgui.yaml
     COUNT: 9000
-DIR_WRK: /home/sosamuli/temp/DataBank/
 PUBLICATION: Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a)
 AUTHORS_CONTACT: Milka Doktorova
 SYSTEM: DLIPC simulation

diff --git a/...a4c610244ec998461b093c395309dc91837e/bf83a4c610244ec998461b093c395309dc91837e/README.yaml b/...a4c610244ec998461b093c395309dc91837e/bf83a4c610244ec998461b093c395309dc91837e/README.yaml
@@ -4,6 +4,8 @@ TRJ:
 - - PM-like.dcd
 PDB:
 - - PM-like.pdb
+PSF:
+- - PM-like.psf
 PREEQTIME: 0
 TIMELEFTOUT: 0
 TEMPERATURE: 310

diff --git a/...eec9b016a1d67b9b618a01aad1e9b6fd0ff8/d9694447765a4eee0db2e36364db29c6aa8d3230/README.yaml b/...eec9b016a1d67b9b618a01aad1e9b6fd0ff8/d9694447765a4eee0db2e36364db29c6aa8d3230/README.yaml
@@ -9,14 +9,12 @@ TIMELEFTOUT: 0
 COMPOSITION:
   POPG:
     NAME: PGR
-    MOLTYPE: system1
     MAPPING: mappingPOPGlipid17.yaml
     COUNT:
     - 187
     - 187
   POPE:
     NAME: PE
-    MOLTYPE: system2
     MAPPING: mappingPOPE_AmberLipid.yaml
     COUNT:
     - 63

diff --git a/...0a356ed12c3697465d9933876dfbef382e98/cf420a356ed12c3697465d9933876dfbef382e98/README.yaml b/...0a356ed12c3697465d9933876dfbef382e98/cf420a356ed12c3697465d9933876dfbef382e98/README.yaml
@@ -14,12 +14,11 @@ COMPOSITION:
     COUNT:
     - 34
     - 38
-DIR_WRK: /home/lara/Databank
 PUBLICATION: null
 AUTHORS_CONTACT: Kav, Batuhan
-SYSTEM: 72POPC_303K
+SYSTEM: 72POPC_303K (equilibriated using Charmm36)
 SOFTWARE_VERSION: 7.4.1
-FF: Charmm-Drude polarizable; system has been equilibriated using Charmm36
+FF: Charmm-Drude polarizable
 FF_SOURCE: null
 FF_DATE: null
 CHK: null
@@ -34,6 +33,6 @@ WARNINGS:
   NOWATER: true
 EXPERIMENT:
   ORDERPARAMETER:
-    POPC: {}
-  FORMFACTOR: {}
+    POPC: []
+  FORMFACTOR: []
 ID: 562
diff --git a/...c4be95331177929f47a2f1c59f2792643901/112cf0742e84e4dbdd3598c8bcc6921f84378fb3/README.yaml b/...c4be95331177929f47a2f1c59f2792643901/112cf0742e84e4dbdd3598c8bcc6921f84378fb3/README.yaml
@@ -14,14 +14,12 @@ DIR_WRK: /media/akiirikk/DATADRIVE1/tietokanta/Data/tmp/DATABANK/tmp_6-935999/
 COMPOSITION:
   POPC:
     NAME: PC
-    MOLTYPE: system1
     MAPPING: mappingPOPC_AmberLipid.yaml
     COUNT:
     - 175
     - 175
   POPG:
     NAME: PGR
-    MOLTYPE: system2
     MAPPING: mappingPOPGlipid17ecc.yaml
     COUNT:
     - 44

diff --git a/...1882481f7f4762372c4977c06b4a1ce3634b/1ea3606eb89db05b49b6e869701993ae39c9d381/README.yaml b/...1882481f7f4762372c4977c06b4a1ce3634b/1ea3606eb89db05b49b6e869701993ae39c9d381/README.yaml
@@ -9,14 +9,12 @@ TIMELEFTOUT: 0
 COMPOSITION:
   POPC:
     NAME: PC
-    MOLTYPE: system1
     MAPPING: mappingPOPC_AmberLipid.yaml
     COUNT:
     - 75
     - 75
   POPG:
     NAME: PGR
-    MOLTYPE: system2
     MAPPING: mappingPOPGlipid17.yaml
     COUNT:
     - 77