Trajectory SP846

Force field: martini_v2.2
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: 19195
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P213 NC01402
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
AVKQPAVVYP
Total charge (e): +1
Number of residues: 10
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 7
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.24
Longitudinal (e nm): 2.09
Transversal (e nm): 0.81
Hydrophobic Dipolar Moment (nm): 1.42
Longitudinal (nm): 1.28
Transversal (nm): 0.6
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
 
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Contacts per residue
(normalized by number of beads in the residue)
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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): 0.642284000 ± 0.000894065
Upper leaflet (nm2): 0.642284000 ± 0.000894065
Lower leaflet (nm2): 0.642284000 ± 0.000894065
Average Z coordinate
Peptide (nm): 5.0247100 ± 0.0343912
First Residue (nm): 4.9951700 ± 0.0360904
Last Residue (nm): 5.0732300 ± 0.0420642
Membrane (nm): 6.84190000 ± 0.00928507
Upper leaflet Head Group (nm): 8.8033000 ± 0.0112076
Lower leaflet Head Group (nm): 4.87909000 ± 0.00740543
Bilayer Thickness (nm): 3.9242100 ± 0.0134332
Peptide insertion (nm): -0.1456190 ± 0.0351795
Contacts
Peptide - Water: 15.205000 ± 0.437729
Peptide - Head groups: 8.485000 ± 0.192001
Peptide - Tail groups: 7.505000 ± 0.221859
Tilt (°): 87.16800 ± 1.73767
PepDF:
5(ns):  CVS
Displacement (nm): 0.8227000 ± 0.0327705
Precession(°): 1.87570 ± 3.51532
50(ns)  CVS
Displacement (nm): 2.530890 ± 0.114558
Precession(°): 12.1375 ± 10.2830
100(ns)  CVS
Displacement(nm): 3.563540 ± 0.170108
Precession(°): 17.3580 ± 13.8974
200(ns)  CVS
Displacement(nm): 5.438910 ± 0.249379
Precession(°): 44.2351 ± 17.6186

  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.