Trajectory SP712

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: 19189
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P146 AP02143
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
SLQMGATAIKQVKKLFKKKGG
Total charge (e): +6
Number of residues: 21
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 11
  Polar: 4
Electrostatic Dipolar Moment (e nm): 1.82
Longitudinal (e nm): 1.41
Transversal (e nm): 1.15
Hydrophobic Dipolar Moment (nm): 6.09
Longitudinal (nm): 6.02
Transversal (nm): 0.88
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)
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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): 0.64354700 ± 0.00104413
Upper leaflet (nm2): 0.64354700 ± 0.00104413
Lower leaflet (nm2): 0.64354700 ± 0.00104413
Average Z coordinate
Peptide (nm): 8.7177200 ± 0.0442833
First Residue (nm): 8.5996300 ± 0.0538777
Last Residue (nm): 8.8929100 ± 0.0543784
Membrane (nm): 6.8212400 ± 0.0106356
Upper leaflet Head Group (nm): 8.7821300 ± 0.0126914
Lower leaflet Head Group (nm): 4.86269000 ± 0.00899323
Bilayer Thickness (nm): 3.9194400 ± 0.0155548
Peptide insertion (nm): -0.0644140 ± 0.0460661
Contacts
Peptide - Water: 30.237500 ± 0.714731
Peptide - Head groups: 13.297500 ± 0.219287
Peptide - Tail groups: 11.512500 ± 0.260587
Tilt (°): 89.49110 ± 1.16912
PepDF:
5(ns):  CVS
Displacement (nm): 0.6742000 ± 0.0284163
Precession(°): -1.12401 ± 1.62522
50(ns)  CVS
Displacement (nm): 1.9228500 ± 0.0883446
Precession(°): -10.75710 ± 4.57575
100(ns)  CVS
Displacement(nm): 2.414800 ± 0.119749
Precession(°): -17.44000 ± 6.32887
200(ns)  CVS
Displacement(nm): 2.675150 ± 0.171484
Precession(°): -21.35880 ± 8.61807

  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.