Trajectory 787

Order parameters quality = N/A

Computational methods Simulation metadata
System POPC/POPE/TOCL mixture
Author(s) Milka Doktorova
Date 05/10/2023
DOI 10.5281/zenodo.13984187
Publication Castillo et al, 2022, Mol. Pharmaceutics. 19:1839-1852 (https://doi.org/10.1021/acs.molpharmaceut.1c00926)
Force field CHARMM36
Simulation length (ps) 570020
Trajectory size 4872398524
Pre-equilibration time 0
Time left out 120
Temperature (K) 310
Number of particles 46290
Software gromacs
Ions SOD(60)
Water TIP3
Lipids - L1 TOCL:POPC:POPE (15:30:15)
Lipids - L2 TOCL:POPC:POPE (15:30:15)
Files View on GitHub main
 Download PDB File
 Link to simulation files
Hover over a component to view composition data.
Upper leaflet
Lower leaflet

Lipids


POPE
  • Quality total: N/A
  • Quality headgroups: N/A
  • Quality tails: N/A
Download Mapping File main
TOCL
  • Quality total: N/A
  • Quality headgroups: N/A
  • Quality tails: N/A
Download Mapping File main
POPC
  • Quality total: N/A
  • Quality headgroups: N/A
  • Quality tails: N/A
Download Mapping File main

Related experiments:

Article DOI Internal ID Type Temperature Actions

Order Parameters POPE

Download JSON main

Group sn-1

Group sn-2

Group headgroup

Group glycerol backbone

Order Parameters TOCL

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Group sn-1 1

Group sn-1 2

Group sn-2 1

Group sn-2 2

Group headgroup

Group glycerol backbone 1

Group glycerol backbone 2

Order Parameters POPC

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Group sn-1

Group sn-2

Group headgroup

Group glycerol backbone

Area per lipid

Form Factor

Experimental and Molecular Dynamics based descriptors

Quality of Order Parameters : N/A
OP Quality of headgroups: N/A
OP Quality of tails: N/A
FF Quality: N/A

Bilayer thickness : 4.2 nm
Area per lipid : 78.3 Å2