Trajectory SP696

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: 19190
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P138 AP01447
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LPGLIAGIAKML
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 11
  Polar: 0
Electrostatic Dipolar Moment (e nm): 1.68
Longitudinal (e nm): 1.54
Transversal (e nm): 0.69
Hydrophobic Dipolar Moment (nm): 1.47
Longitudinal (nm): 0.83
Transversal (nm): 1.21
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): 0.643099000 ± 0.000847812
Upper leaflet (nm2): 0.643099000 ± 0.000847812
Lower leaflet (nm2): 0.643099000 ± 0.000847812
Average Z coordinate
Peptide (nm): 8.4540600 ± 0.0365624
First Residue (nm): 8.4347400 ± 0.0430714
Last Residue (nm): 8.4130900 ± 0.0541136
Membrane (nm): 6.83101000 ± 0.00889645
Upper leaflet Head Group (nm): 8.7936200 ± 0.0105987
Lower leaflet Head Group (nm): 4.87031000 ± 0.00714965
Bilayer Thickness (nm): 3.9233100 ± 0.0127847
Peptide insertion (nm): -0.3395630 ± 0.0380676
Contacts
Peptide - Water: 13.617500 ± 0.469327
Peptide - Head groups: 8.265000 ± 0.214292
Peptide - Tail groups: 8.6825 ± 0.2319
Tilt (°): 90.6163 ± 1.8895
PepDF:
5(ns):  CVS
Displacement (nm): 0.8067300 ± 0.0339835
Precession(°): 3.53473 ± 3.43975
50(ns)  CVS
Displacement (nm): 2.391520 ± 0.104737
Precession(°): 36.8831 ± 10.2948
100(ns)  CVS
Displacement(nm): 3.316100 ± 0.135808
Precession(°): 83.3895 ± 14.3229
200(ns)  CVS
Displacement(nm): 5.053430 ± 0.175512
Precession(°): 205.0590 ± 17.1636

  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.