Trajectory SP1227

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: P402 AP01010
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
MWSGMWRRKLKKLRNALKKKLKGE
Total charge (e): +9
Number of residues: 24
By amino acid:
  Basic: 10
  Acidic: 1
  Hydrophobic: 11
  Polar: 2
Electrostatic Dipolar Moment (e nm): 5.29
Longitudinal (e nm): 4.66
Transversal (e nm): 2.5
Hydrophobic Dipolar Moment (nm): 10.73
Longitudinal (nm): 10.48
Transversal (nm): 2.33
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): 0.61411900 ± 0.00099642
Upper leaflet (nm2): 0.61411900 ± 0.00099642
Lower leaflet (nm2): 0.61411900 ± 0.00099642
Average Z coordinate
Peptide (nm): 4.1340800 ± 0.0373462
First Residue (nm): 4.3034900 ± 0.0536685
Last Residue (nm): 3.8563100 ± 0.0468026
Membrane (nm): 6.4019900 ± 0.0101974
Upper leaflet Head Group (nm): 8.4137400 ± 0.0122749
Lower leaflet Head Group (nm): 4.3902800 ± 0.0083479
Bilayer Thickness (nm): 4.0234700 ± 0.0148445
Peptide insertion (nm): 0.2561940 ± 0.0382678
Contacts
Peptide - Water: 59.757500 ± 0.914138
Peptide - Head groups: 14.262500 ± 0.354147
Peptide - Tail groups: 11.480000 ± 0.294405
Tilt (°): 80.26320 ± 1.07388
PepDF:
5(ns):  CVS
Displacement (nm): 0.6659880 ± 0.0268243
Precession(°): 0.476659 ± 1.602390
50(ns)  CVS
Displacement (nm): 1.9702600 ± 0.0905335
Precession(°): -0.75008 ± 4.55359
100(ns)  CVS
Displacement(nm): 2.957890 ± 0.122688
Precession(°): -4.65510 ± 6.03102
200(ns)  CVS
Displacement(nm): 4.330610 ± 0.180442
Precession(°): -8.29071 ± 7.95926

  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.