Trajectory SP1141

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: 45468
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P360 NC02212
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
KLALKLALKAWKAALKLA
Total charge (e): +5
Number of residues: 18
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 13
  Polar: 0
Electrostatic Dipolar Moment (e nm): 4.95
Longitudinal (e nm): 4.57
Transversal (e nm): 1.9
Hydrophobic Dipolar Moment (nm): 1.03
Longitudinal (nm): 0.42
Transversal (nm): 0.94
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): 0.6496170 ± 0.0010847
Upper leaflet (nm2): 0.6496170 ± 0.0010847
Lower leaflet (nm2): 0.6496170 ± 0.0010847
Average Z coordinate
Peptide (nm): 4.704560 ± 0.030427
First Residue (nm): 4.7620700 ± 0.0332958
Last Residue (nm): 4.7499400 ± 0.0487194
Membrane (nm): 6.567430 ± 0.010868
Upper leaflet Head Group (nm): 8.534730 ± 0.012994
Lower leaflet Head Group (nm): 4.59910000 ± 0.00866802
Bilayer Thickness (nm): 3.9356300 ± 0.0156198
Peptide insertion (nm): -0.1054590 ± 0.0316376
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 12.192500 ± 0.308184
Peptide - Tail groups: 10.842500 ± 0.247382
Tilt (°): 86.56020 ± 1.14559
PepDF:
5(ns):  CVS
Displacement (nm): 0.623651 ± 0.026626
Precession(°): -1.03577 ± 1.46321
50(ns)  CVS
Displacement (nm): 2.1330000 ± 0.0985579
Precession(°): -7.91618 ± 5.48221
100(ns)  CVS
Displacement(nm): 3.229710 ± 0.149087
Precession(°): -11.38260 ± 7.44141
200(ns)  CVS
Displacement(nm): 5.154240 ± 0.233983
Precession(°): -27.50420 ± 8.28052

  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.