Trajectory SP1359

Force field: martini_v3
Simulation length (ns): 5000
Electric field (kJ mol-1 nm-1 e-1): 0
Temperature (K): 300 (v-rescale)
Pressure (bar): 1 (Parrinello-rahman semiisotropic)
Number of particles: 17404
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P468 AP03942
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
PFLLSLIPSAISALKKL
Total charge (e): +2
Number of residues: 17
By amino acid:
  Basic: 2
  Acidic: 0
  Hydrophobic: 12
  Polar: 3
Electrostatic Dipolar Moment (e nm): 1.47
Longitudinal (e nm): 1.19
Transversal (e nm): 0.87
Hydrophobic Dipolar Moment (nm): 5.37
Longitudinal (nm): 5.08
Transversal (nm): 1.74
Secondary structure: Helix
Activity:

Download Files
  ITP file.
  JSON file.
  PDB file.

Click on any component to highlight it from the plot.
Upper leaflet
Lower leaflet

Lipids


Membrane model for: POPG:POPE (1:3) (Gram-negative bacteria)

POPE
1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Total charge (e): 0

  See POPE lipid
  Download ITP File.
  Download PDB File.
POPG
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Total charge (e): -1

  See POPG lipid
  Download ITP File.
  Download PDB File.
Last snapshot
  Download PDB File.
Total contacts per residue
 
  Download PDB File.
Contacts per residue
(normalized by number of beads in the residue)
  Download PDB File.

Molecular Dynamics based descriptors
Average and standard deviation, calculated using the autocorrelation function (for time series) or the width of the distribution, for the last microsecond of the trajectory

Area per lipid
Membrane (nm2): 0.615564000 ± 0.000951128
Upper leaflet (nm2): 0.615564000 ± 0.000951128
Lower leaflet (nm2): 0.615564000 ± 0.000951128
Average Z coordinate
Peptide (nm): 4.450560 ± 0.041408
First Residue (nm): 4.498650 ± 0.046938
Last Residue (nm): 4.1685000 ± 0.0602543
Membrane (nm): 6.39012000 ± 0.00953463
Upper leaflet Head Group (nm): 8.4011400 ± 0.0116269
Lower leaflet Head Group (nm): 4.37850000 ± 0.00764757
Bilayer Thickness (nm): 4.0226400 ± 0.0139165
Peptide insertion (nm): -0.0720561 ± 0.0421083
Contacts
Peptide - Water: 28.297500 ± 0.772308
Peptide - Head groups: 9.872500 ± 0.286763
Peptide - Tail groups: 10.802500 ± 0.237511
Tilt (°): 78.02010 ± 1.52991
PepDF:
5(ns):  CVS
Displacement (nm): 0.7223130 ± 0.0306135
Precession(°): -0.267085 ± 2.343810
50(ns)  CVS
Displacement (nm): 2.00896 ± 0.10780
Precession(°): 0.0108034 ± 8.8670600
100(ns)  CVS
Displacement(nm): 2.904240 ± 0.153049
Precession(°): 2.20763 ± 14.86220
200(ns)  CVS
Displacement(nm): 3.474880 ± 0.178978
Precession(°): -5.15198 ± 26.68310

  Download JSON File.

Peptide Analyses

Peptide Displacement Fingerprint (PepDF)
Lateral displacement vs Rotational Displacement along the trajectory, for different time windows .

Density maps:
2D-density maps of lipids around the peptide along XY and YZ axis, calculated for each lipid type along the last microsecond.

Lipid-Peptide Analyses:

z-Position
Z-coordinate, averaged for differetn parts of the the system: peptide, membrane, first and last backbone (BB) residues and upper of lower leaflet lipids’ headgroups (HGs).
Minimum distance
Minimum distance (nm) between the peptide backbone and the lipids (headgroups and tailgroups).
Number of contacts
Number of contacts between the peptide backbone and the water or the lipids separated by lipid headgroups (HG) or lipid tails, using a cut-off of 0.6 nm.
Lateral density
Lateral density for the different components of the system: headgroups, tail groups, peptide and water.