Trajectory SP1360

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: 19211
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P469 AP04269
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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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: POPC (Healthy mammal)

POPC
2-oleoyl-sn-glycero-3-phosphocholine
Total charge (e): 0

  See POPC 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): 0.64920200 ± 0.00128431
Upper leaflet (nm2): 0.64920200 ± 0.00128431
Lower leaflet (nm2): 0.64920200 ± 0.00128431
Average Z coordinate
Peptide (nm): 8.7548400 ± 0.0388254
First Residue (nm): 8.6528100 ± 0.0493916
Last Residue (nm): 8.803730 ± 0.043305
Membrane (nm): 6.8308400 ± 0.0135547
Upper leaflet Head Group (nm): 8.7721900 ± 0.0159838
Lower leaflet Head Group (nm): 4.8901700 ± 0.0110141
Bilayer Thickness (nm): 3.8820100 ± 0.0194112
Peptide insertion (nm): -0.0173426 ± 0.0419868
Contacts
Peptide - Water: 26.947500 ± 0.665898
Peptide - Head groups: 8.795000 ± 0.266179
Peptide - Tail groups: 9.047500 ± 0.302551
Tilt (°): 84.97070 ± 1.63553
PepDF:
5(ns):  CVS
Displacement (nm): 0.8412020 ± 0.0331207
Precession(°): 0.313627 ± 3.311950
50(ns)  CVS
Displacement (nm): 2.817190 ± 0.125175
Precession(°): 10.8546 ± 12.4617
100(ns)  CVS
Displacement(nm): 3.872040 ± 0.216429
Precession(°): 37.9587 ± 16.9776
200(ns)  CVS
Displacement(nm): 5.596620 ± 0.399368
Precession(°): 71.4807 ± 23.4595

  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.