Trajectory 618

Order parameters quality = N/A

Computational methods Simulation metadata
System 250POPC_50POPS_11174SOL_50SOD_189CAL_378CLA_320K
Author(s) Nencini, Ricky
Date 01/10/2021
DOI 10.5281/zenodo.3371327
Publication N/A
Force field CHARMM36 with NBFIX for calcium ions
Simulation length (ps) 436600
Trajectory size 1208113740
Pre-equilibration time 0
Time left out 137
Temperature (K) 320
Number of particles 73989
Software gromacs
Ions CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50), CLA(378), CAL(189), SOD(50)
Water TIP3
Lipids - L1 POPS:POPC (25:125)
Lipids - L2 POPS:POPC (25:125)
Files View on GitHub main
 Download PDB File
 Link to simulation files
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Upper leaflet
Lower leaflet

Lipids


POPS
  • 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 POPS

Download JSON main

Group sn-1

Group sn-2

Group headgroup

Group glycerol backbone

Order Parameters POPC

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 : 4.4 nm
Area per lipid : 62.8 Å2