Trajectory SP1361

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: 17401
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P469 AP04269
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
ILGKLWKGVKSIF
Total charge (e): +3
Number of residues: 13
By amino acid:
  Basic: 3
  Acidic: 0
  Hydrophobic: 9
  Polar: 1
Electrostatic Dipolar Moment (e nm): 3.34
Longitudinal (e nm): 2.96
Transversal (e nm): 1.55
Hydrophobic Dipolar Moment (nm): 1.5
Longitudinal (nm): 0.46
Transversal (nm): 1.43
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): 0.614747000 ± 0.000812454
Upper leaflet (nm2): 0.614747000 ± 0.000812454
Lower leaflet (nm2): 0.614747000 ± 0.000812454
Average Z coordinate
Peptide (nm): 8.3967200 ± 0.0388729
First Residue (nm): 8.3031100 ± 0.0487748
Last Residue (nm): 8.4562000 ± 0.0446815
Membrane (nm): 6.39825000 ± 0.00829441
Upper leaflet Head Group (nm): 8.4122000 ± 0.0102287
Lower leaflet Head Group (nm): 4.38493000 ± 0.00667299
Bilayer Thickness (nm): 4.0272700 ± 0.0122129
Peptide insertion (nm): -0.0154835 ± 0.0401961
Contacts
Peptide - Water: 26.190000 ± 0.810123
Peptide - Head groups: 9.03500 ± 0.27687
Peptide - Tail groups: 9.302500 ± 0.293089
Tilt (°): 84.78310 ± 1.77015
PepDF:
5(ns):  CVS
Displacement (nm): 0.7397510 ± 0.0336501
Precession(°): -2.13462 ± 2.98031
50(ns)  CVS
Displacement (nm): 2.11181 ± 0.11295
Precession(°): -17.22400 ± 9.92412
100(ns)  CVS
Displacement(nm): 2.843590 ± 0.148697
Precession(°): -34.9359 ± 15.0387
200(ns)  CVS
Displacement(nm): 3.655070 ± 0.156666
Precession(°): -91.7229 ± 23.3475

  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.