Trajectory SP740

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: 19187
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P160 AP02901
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
SENGKCNLLCLVKKKLRAVGNVIKTVVGKIA
Total charge (e): +6
Number of residues: 31
By amino acid:
  Basic: 7
  Acidic: 1
  Hydrophobic: 16
  Polar: 7
Electrostatic Dipolar Moment (e nm): 3.58
Longitudinal (e nm): 3.47
Transversal (e nm): 0.88
Hydrophobic Dipolar Moment (nm): 5.72
Longitudinal (nm): 5.37
Transversal (nm): 1.95
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): 0.644586000 ± 0.000964418
Upper leaflet (nm2): 0.644586000 ± 0.000964418
Lower leaflet (nm2): 0.644586000 ± 0.000964418
Average Z coordinate
Peptide (nm): 4.9277000 ± 0.0236499
First Residue (nm): 4.8278800 ± 0.0331536
Last Residue (nm): 4.9883300 ± 0.0380755
Membrane (nm): 6.8095300 ± 0.0097347
Upper leaflet Head Group (nm): 8.7657000 ± 0.0117673
Lower leaflet Head Group (nm): 4.85001000 ± 0.00787524
Bilayer Thickness (nm): 3.9156900 ± 0.0141594
Peptide insertion (nm): -0.0776948 ± 0.0249266
Contacts
Peptide - Water: 40.722500 ± 0.789574
Peptide - Head groups: 17.662500 ± 0.273833
Peptide - Tail groups: 14.902500 ± 0.309461
Tilt (°): 93.119900 ± 0.699538
PepDF:
5(ns):  CVS
Displacement (nm): 0.6193740 ± 0.0247675
Precession(°): 0.876753 ± 1.100680
50(ns)  CVS
Displacement (nm): 1.6201900 ± 0.0851824
Precession(°): 8.27194 ± 3.96792
100(ns)  CVS
Displacement(nm): 2.1119200 ± 0.0996793
Precession(°): 15.33440 ± 6.16659
200(ns)  CVS
Displacement(nm): 1.9803300 ± 0.0897906
Precession(°): 43.06650 ± 8.44911

  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.