Trajectory 772

Order parameters quality = N/A

Computational methods Simulation metadata
System POPC/TOCL mixture
Author(s) Milka Doktorova
Date 25/09/2023
DOI 10.5281/zenodo.13984201
Publication Castillo et al, 2022, Mol. Pharmaceutics. 19:1839-1852 (https://doi.org/10.1021/acs.molpharmaceut.1c00926)
Force field CHARMM36
Simulation length (ps) 530020
Trajectory size 5766486676
Pre-equilibration time 0
Time left out 30
Temperature (K) 310
Number of particles 58500
Software gromacs
Ions SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120), SOD(120)
Water TIP3
Lipids - L1 TOCL:POPE (30:30)
Lipids - L2 TOCL:POPE (30:30)
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

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

Download JSON main

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

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 : 4.1 nm
Area per lipid : 94.6 Å2