Trajectory 3

Order parameters quality = N/A

Computational methods Simulation metadata
System DMPC/liverPI bilayer
Author(s) Matti Javanainen (), Hector Martinez-Seara ()
Date 01/10/2021
DOI 10.5281/zenodo.4651415
Publication N/A
Force field CHARMM36
Simulation length (ps) 2000100
Trajectory size 5194468496
Pre-equilibration time 0
Time left out 500
Temperature (K) 303.15
Number of particles 70516
Software gromacs
Ions CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104), CLA(28), SOD(104)
Water TIP3
Lipids - L1 DMPC:SAPI:POPI:SLPI (90:23:8:7)
Lipids - L2 DMPC:SAPI:POPI:SLPI (90:23:8:7)
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


DMPC
  • Quality total: N/A
  • Quality headgroups: N/A
  • Quality tails: N/A
Download Mapping File main
SAPI
  • Quality total: N/A
  • Quality headgroups: N/A
  • Quality tails: N/A
Download Mapping File main
POPI
  • Quality total: N/A
  • Quality headgroups: N/A
  • Quality tails: N/A
Download Mapping File main
SLPI
  • 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 DMPC

Download JSON main

Group sn-1

Group sn-2

Group headgroup

Group glycerol backbone

Order Parameters SAPI

Download JSON main

Group sn-1

Group sn-2

Group headgroup

Group glycerol backbone

Order Parameters POPI

Download JSON main

Group sn-1

Group sn-2

Group headgroup

Group glycerol backbone

Order Parameters SLPI

Download JSON main

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 : 60.6 Å2