Trajectory SP1310

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: 19207
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P444 AP03258
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LPLIAGLFGKIF
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 11
  Polar: 0
Electrostatic Dipolar Moment (e nm): 1.75
Longitudinal (e nm): 1.59
Transversal (e nm): 0.72
Hydrophobic Dipolar Moment (nm): 1.28
Longitudinal (nm): 0.97
Transversal (nm): 0.84
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): 0.64963400 ± 0.00110638
Upper leaflet (nm2): 0.64963400 ± 0.00110638
Lower leaflet (nm2): 0.64963400 ± 0.00110638
Average Z coordinate
Peptide (nm): 8.4876200 ± 0.0411202
First Residue (nm): 8.5988000 ± 0.0469421
Last Residue (nm): 8.6930000 ± 0.0467121
Membrane (nm): 6.8279900 ± 0.0110118
Upper leaflet Head Group (nm): 8.770480 ± 0.013181
Lower leaflet Head Group (nm): 4.88677000 ± 0.00915218
Bilayer Thickness (nm): 3.8837000 ± 0.0160469
Peptide insertion (nm): -0.2828570 ± 0.0431811
Contacts
Peptide - Water: 17.917500 ± 0.666715
Peptide - Head groups: 8.750000 ± 0.245465
Peptide - Tail groups: 9.517500 ± 0.268363
Tilt (°): 88.03030 ± 1.62404
PepDF:
5(ns):  CVS
Displacement (nm): 0.8475520 ± 0.0370036
Precession(°): -3.45311 ± 3.57127
50(ns)  CVS
Displacement (nm): 2.550630 ± 0.120196
Precession(°): -36.5578 ± 12.1917
100(ns)  CVS
Displacement(nm): 3.635710 ± 0.165603
Precession(°): -71.0087 ± 18.6486
200(ns)  CVS
Displacement(nm): 4.747640 ± 0.202814
Precession(°): -121.9840 ± 23.3313

  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.