Trajectory SP1294

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: 19218
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P436 AP03013
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
NPLKLFLPSTWVHFFKFLR
Total charge (e): +3
Number of residues: 19
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 12
  Polar: 3
Electrostatic Dipolar Moment (e nm): 2.86
Longitudinal (e nm): 2.64
Transversal (e nm): 1.08
Hydrophobic Dipolar Moment (nm): 1.22
Longitudinal (nm): 0.58
Transversal (nm): 1.07
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): 0.65018600 ± 0.00119908
Upper leaflet (nm2): 0.65018600 ± 0.00119908
Lower leaflet (nm2): 0.65018600 ± 0.00119908
Average Z coordinate
Peptide (nm): 4.8954900 ± 0.0403759
First Residue (nm): 4.7208900 ± 0.0522529
Last Residue (nm): 4.5995800 ± 0.0484236
Membrane (nm): 6.8193500 ± 0.0124067
Upper leaflet Head Group (nm): 8.7580400 ± 0.0147745
Lower leaflet Head Group (nm): 4.8792800 ± 0.0100362
Bilayer Thickness (nm): 3.8787600 ± 0.0178609
Peptide insertion (nm): -0.0162082 ± 0.0416046
Contacts
Peptide - Water: 38.63750 ± 0.85592
Peptide - Head groups: 11.79750 ± 0.31651
Peptide - Tail groups: 11.532500 ± 0.323621
Tilt (°): 86.65300 ± 1.33575
PepDF:
5(ns):  CVS
Displacement (nm): 0.7631690 ± 0.0306101
Precession(°): -1.17077 ± 2.33458
50(ns)  CVS
Displacement (nm): 2.119880 ± 0.108947
Precession(°): -13.72560 ± 7.13001
100(ns)  CVS
Displacement(nm): 2.702690 ± 0.151116
Precession(°): -28.7988 ± 10.0076
200(ns)  CVS
Displacement(nm): 3.580000 ± 0.174208
Precession(°): -56.34960 ± 8.75775

  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.