Trajectory SP1403

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: 17395
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P490 NC01594
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
YGRRARRAARR
Total charge (e): +6
Number of residues: 11
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 4
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.91
Longitudinal (e nm): 2.12
Transversal (e nm): 2
Hydrophobic Dipolar Moment (nm): 1.62
Longitudinal (nm): 1.46
Transversal (nm): 0.69
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): 0.613481000 ± 0.000991634
Upper leaflet (nm2): 0.613481000 ± 0.000991634
Lower leaflet (nm2): 0.613481000 ± 0.000991634
Average Z coordinate
Peptide (nm): 6.35628 ± 1.79433
First Residue (nm): 6.32165 ± 1.68876
Last Residue (nm): 6.39006 ± 1.93291
Membrane (nm): 6.4125000 ± 0.0100729
Upper leaflet Head Group (nm): 8.4275900 ± 0.0123542
Lower leaflet Head Group (nm): 4.39705000 ± 0.00823561
Bilayer Thickness (nm): 4.0305400 ± 0.0148476
Peptide insertion (nm): -1.95923 ± 1.79434
Contacts
Peptide - Water: 54.06250 ± 4.27777
Peptide - Head groups: 4.15000 ± 1.60152
Peptide - Tail groups: 1.64750 ± 0.85877
Tilt (°): 75.32620 ± 7.62168
PepDF:
5(ns):  CVS
Displacement (nm): 1.3513000 ± 0.0699288
Precession(°): 22.6068 ± 17.5453
50(ns)  CVS
Displacement (nm): 3.508270 ± 0.191478
Precession(°): 241.063 ± 56.622
100(ns)  CVS
Displacement(nm): 5.162950 ± 0.243141
Precession(°): 514.6310 ± 69.9168
200(ns)  CVS
Displacement(nm): 8.604360 ± 0.331805
Precession(°): 1064.660 ± 116.948

  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.