Trajectory SP748

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: P164 AP03059
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
IVPSIFLLKKAFCIALKKC
Total charge (e): +4
Number of residues: 19
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 12
  Polar: 3
Electrostatic Dipolar Moment (e nm): 2.08
Longitudinal (e nm): 1.78
Transversal (e nm): 1.08
Hydrophobic Dipolar Moment (nm): 4.67
Longitudinal (nm): 4.56
Transversal (nm): 1
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): 0.644639000 ± 0.000987934
Upper leaflet (nm2): 0.644639000 ± 0.000987934
Lower leaflet (nm2): 0.644639000 ± 0.000987934
Average Z coordinate
Peptide (nm): 8.4865600 ± 0.0377309
First Residue (nm): 8.344700 ± 0.050658
Last Residue (nm): 8.6108000 ± 0.0426564
Membrane (nm): 6.8084500 ± 0.0103321
Upper leaflet Head Group (nm): 8.76874 ± 0.01239
Lower leaflet Head Group (nm): 4.85169000 ± 0.00844122
Bilayer Thickness (nm): 3.9170500 ± 0.0149922
Peptide insertion (nm): -0.2821750 ± 0.0397131
Contacts
Peptide - Water: 23.910000 ± 0.638835
Peptide - Head groups: 12.575000 ± 0.288719
Peptide - Tail groups: 12.602500 ± 0.306966
Tilt (°): 82.2282 ± 1.1765
PepDF:
5(ns):  CVS
Displacement (nm): 0.7173140 ± 0.0311931
Precession(°): 0.401831 ± 1.837360
50(ns)  CVS
Displacement (nm): 2.001650 ± 0.108275
Precession(°): 2.85506 ± 5.74360
100(ns)  CVS
Displacement(nm): 2.609400 ± 0.149728
Precession(°): 2.79116 ± 8.19760
200(ns)  CVS
Displacement(nm): 3.275410 ± 0.209488
Precession(°): 10.2290 ± 11.4187

  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.