Trajectory SP676

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: 19185
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P128 AP01010
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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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): 5.48
Longitudinal (e nm): 4.94
Transversal (e nm): 2.37
Hydrophobic Dipolar Moment (nm): 10.69
Longitudinal (nm): 10.41
Transversal (nm): 2.43
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
 
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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): 0.64429100 ± 0.00098086
Upper leaflet (nm2): 0.64429100 ± 0.00098086
Lower leaflet (nm2): 0.64429100 ± 0.00098086
Average Z coordinate
Peptide (nm): 8.8050500 ± 0.0329373
First Residue (nm): 8.7183300 ± 0.0491753
Last Residue (nm): 8.9861800 ± 0.0391364
Membrane (nm): 6.8085300 ± 0.0105917
Upper leaflet Head Group (nm): 8.7670600 ± 0.0123076
Lower leaflet Head Group (nm): 4.85170000 ± 0.00851635
Bilayer Thickness (nm): 3.9153500 ± 0.0149668
Peptide insertion (nm): 0.0379954 ± 0.0351616
Contacts
Peptide - Water: 42.017500 ± 0.762459
Peptide - Head groups: 16.157500 ± 0.350885
Peptide - Tail groups: 12.770000 ± 0.305791
Tilt (°): 83.383900 ± 0.987729
PepDF:
5(ns):  CVS
Displacement (nm): 0.633622 ± 0.028002
Precession(°): -0.708972 ± 1.424500
50(ns)  CVS
Displacement (nm): 1.9329900 ± 0.0955342
Precession(°): -6.78802 ± 4.32207
100(ns)  CVS
Displacement(nm): 2.513760 ± 0.116368
Precession(°): -13.79850 ± 6.62565
200(ns)  CVS
Displacement(nm): 3.825630 ± 0.145705
Precession(°): -16.68710 ± 9.71395

  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.