Trajectory SP1248

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: 19213
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P413 AP01448
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LPIALKALGSIFPKIL
Total charge (e): +2
Number of residues: 16
By amino acid:
  Basic: 2
  Acidic: 0
  Hydrophobic: 13
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.73
Longitudinal (e nm): 2.57
Transversal (e nm): 0.91
Hydrophobic Dipolar Moment (nm): 1.11
Longitudinal (nm): 0.19
Transversal (nm): 1.09
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): 0.64974300 ± 0.00107416
Upper leaflet (nm2): 0.64974300 ± 0.00107416
Lower leaflet (nm2): 0.64974300 ± 0.00107416
Average Z coordinate
Peptide (nm): 4.9292700 ± 0.0314701
First Residue (nm): 4.9125300 ± 0.0421331
Last Residue (nm): 4.8739300 ± 0.0496272
Membrane (nm): 6.8288700 ± 0.0113857
Upper leaflet Head Group (nm): 8.7691400 ± 0.0133483
Lower leaflet Head Group (nm): 4.88764000 ± 0.00947742
Bilayer Thickness (nm): 3.8815000 ± 0.0163707
Peptide insertion (nm): -0.0416272 ± 0.0328662
Contacts
Peptide - Water: 27.332500 ± 0.646748
Peptide - Head groups: 9.242500 ± 0.256805
Peptide - Tail groups: 9.820000 ± 0.244316
Tilt (°): 90.85090 ± 1.75862
PepDF:
5(ns):  CVS
Displacement (nm): 0.8487750 ± 0.0348509
Precession(°): 1.77861 ± 2.82553
50(ns)  CVS
Displacement (nm): 2.362790 ± 0.114687
Precession(°): 23.28090 ± 9.38473
100(ns)  CVS
Displacement(nm): 3.020920 ± 0.142025
Precession(°): 42.8251 ± 14.3171
200(ns)  CVS
Displacement(nm): 3.702410 ± 0.178827
Precession(°): 95.4975 ± 22.6237

  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.