Trajectory SP1318

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: 19212
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P448 AP03427
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LWKTLLKNVGKAAGKAVLNAVTDMVNQ
Total charge (e): +3
Number of residues: 27
By amino acid:
  Basic: 4
  Acidic: 1
  Hydrophobic: 16
  Polar: 6
Electrostatic Dipolar Moment (e nm): 9.78
Longitudinal (e nm): 9.59
Transversal (e nm): 1.89
Hydrophobic Dipolar Moment (nm): 5.7
Longitudinal (nm): 5.63
Transversal (nm): 0.88
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): 0.649328000 ± 0.000910626
Upper leaflet (nm2): 0.649328000 ± 0.000910626
Lower leaflet (nm2): 0.649328000 ± 0.000910626
Average Z coordinate
Peptide (nm): 4.5708300 ± 0.0374648
First Residue (nm): 4.9178800 ± 0.0458541
Last Residue (nm): 4.2244600 ± 0.0617974
Membrane (nm): 6.8242400 ± 0.0097391
Upper leaflet Head Group (nm): 8.7639100 ± 0.0116506
Lower leaflet Head Group (nm): 4.88568000 ± 0.00792276
Bilayer Thickness (nm): 3.8782300 ± 0.0140892
Peptide insertion (nm): 0.3148450 ± 0.0382934
Contacts
Peptide - Water: 58.14000 ± 1.62583
Peptide - Head groups: 12.840000 ± 0.379224
Peptide - Tail groups: 11.170000 ± 0.434053
Tilt (°): 78.73890 ± 1.27899
PepDF:
5(ns):  CVS
Displacement (nm): 0.7670840 ± 0.0312758
Precession(°): -1.66653 ± 1.89435
50(ns)  CVS
Displacement (nm): 2.720930 ± 0.114876
Precession(°): -15.93060 ± 6.20427
100(ns)  CVS
Displacement(nm): 4.007350 ± 0.165414
Precession(°): -34.4538 ± 10.3842
200(ns)  CVS
Displacement(nm): 5.456950 ± 0.204555
Precession(°): -51.9576 ± 18.1337

  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.