Trajectory SP1057

Force field: martini_v2.2P
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: 45473
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P318 AP03654
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
WLRRIKAWLRRIKA
Total charge (e): +6
Number of residues: 14
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 8
  Polar: 0
Electrostatic Dipolar Moment (e nm): 3.08
Longitudinal (e nm): 2.45
Transversal (e nm): 1.86
Hydrophobic Dipolar Moment (nm): 3.29
Longitudinal (nm): 2.97
Transversal (nm): 1.42
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): 0.64870400 ± 0.00103911
Upper leaflet (nm2): 0.64870400 ± 0.00103911
Lower leaflet (nm2): 0.64870400 ± 0.00103911
Average Z coordinate
Peptide (nm): 4.5984700 ± 0.0320596
First Residue (nm): 4.7269300 ± 0.0415069
Last Residue (nm): 4.4078300 ± 0.0336002
Membrane (nm): 6.5774000 ± 0.0104603
Upper leaflet Head Group (nm): 8.5463900 ± 0.0125915
Lower leaflet Head Group (nm): 4.60728000 ± 0.00835249
Bilayer Thickness (nm): 3.9391100 ± 0.0151099
Peptide insertion (nm): 0.00880625 ± 0.03312980
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 10.85250 ± 0.31337
Peptide - Tail groups: 9.385000 ± 0.229394
Tilt (°): 87.93290 ± 1.21666
PepDF:
5(ns):  CVS
Displacement (nm): 0.6574760 ± 0.0264129
Precession(°): 0.309125 ± 1.861510
50(ns)  CVS
Displacement (nm): 1.9025200 ± 0.0972699
Precession(°): 7.01739 ± 5.35084
100(ns)  CVS
Displacement(nm): 2.907980 ± 0.158746
Precession(°): 11.94100 ± 6.41809
200(ns)  CVS
Displacement(nm): 3.644860 ± 0.239624
Precession(°): 23.6367 ± 8.7258

  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.