Trajectory SP649

Force field: martini_v2.2
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: 17387
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P114 AP00144
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
IGKFLHSAKKFGKAFVGEIMNS
Total charge (e): +3
Number of residues: 22
By amino acid:
  Basic: 7
  Acidic: 1
  Hydrophobic: 13
  Polar: 3
Electrostatic Dipolar Moment (e nm): 7.32
Longitudinal (e nm): 6.94
Transversal (e nm): 2.31
Hydrophobic Dipolar Moment (nm): 2.12
Longitudinal (nm): 1.42
Transversal (nm): 1.58
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): 0.606591000 ± 0.000858994
Upper leaflet (nm2): 0.606591000 ± 0.000858994
Lower leaflet (nm2): 0.606591000 ± 0.000858994
Average Z coordinate
Peptide (nm): 8.5495400 ± 0.0413347
First Residue (nm): 8.4015100 ± 0.0402399
Last Residue (nm): 8.6675600 ± 0.0564809
Membrane (nm): 6.5156000 ± 0.0092351
Upper leaflet Head Group (nm): 8.5426200 ± 0.0111069
Lower leaflet Head Group (nm): 4.49023000 ± 0.00753087
Bilayer Thickness (nm): 4.0523900 ± 0.0134193
Peptide insertion (nm): 0.00691575 ± 0.04280090
Contacts
Peptide - Water: 32.790000 ± 0.930685
Peptide - Head groups: 14.445000 ± 0.323246
Peptide - Tail groups: 12.500000 ± 0.250325
Tilt (°): 87.033300 ± 0.989992
PepDF:
5(ns):  CVS
Displacement (nm): 0.6466660 ± 0.0269751
Precession(°): -0.151843 ± 1.447060
50(ns)  CVS
Displacement (nm): 1.8858400 ± 0.0816037
Precession(°): 0.791207 ± 4.030930
100(ns)  CVS
Displacement(nm): 2.518960 ± 0.121322
Precession(°): 3.06966 ± 4.62704
200(ns)  CVS
Displacement(nm): 3.446220 ± 0.179509
Precession(°): 3.16558 ± 5.77218

  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.