Trajectory SP1006

Force field: martini_v2.2P
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: 39841
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P292 AP02662
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

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Sequence :
PHKKKLAVYPVFLFYLFLSWFSLIV
Total charge (e): +3
Number of residues: 25
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 17
  Polar: 4
Electrostatic Dipolar Moment (e nm): 9.03
Longitudinal (e nm): 9.02
Transversal (e nm): 0.53
Hydrophobic Dipolar Moment (nm): 14.99
Longitudinal (nm): 14.97
Transversal (nm): 0.78
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)
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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): 0.638143000 ± 0.000998654
Upper leaflet (nm2): 0.638143000 ± 0.000998654
Lower leaflet (nm2): 0.638143000 ± 0.000998654
Average Z coordinate
Peptide (nm): 7.7789600 ± 0.0359006
First Residue (nm): 8.1157600 ± 0.0452245
Last Residue (nm): 7.6595900 ± 0.0495453
Membrane (nm): 6.0274800 ± 0.0092407
Upper leaflet Head Group (nm): 8.0222100 ± 0.0113655
Lower leaflet Head Group (nm): 4.0378500 ± 0.0073228
Bilayer Thickness (nm): 3.9843600 ± 0.0135202
Peptide insertion (nm): -0.2432540 ± 0.0376567
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 16.105000 ± 0.295117
Peptide - Tail groups: 16.64500 ± 0.37351
Tilt (°): 93.70880 ± 1.00606
PepDF:
5(ns):  CVS
Displacement (nm): 0.522495 ± 0.022698
Precession(°): -0.0662881 ± 0.9205590
50(ns)  CVS
Displacement (nm): 1.5431300 ± 0.0730483
Precession(°): -0.19432 ± 3.25719
100(ns)  CVS
Displacement(nm): 2.045330 ± 0.110122
Precession(°): -0.341593 ± 5.171980
200(ns)  CVS
Displacement(nm): 2.922240 ± 0.145723
Precession(°): -2.43977 ± 8.30664

  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.