Trajectory SP818

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: 19193
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P199 NC00188
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
CKRKGSSCRRTSYDCCTGSCRNGKC
Total charge (e): +6
Number of residues: 25
By amino acid:
  Basic: 7
  Acidic: 1
  Hydrophobic: 3
  Polar: 14
Electrostatic Dipolar Moment (e nm): 8.65
Longitudinal (e nm): 8.48
Transversal (e nm): 1.7
Hydrophobic Dipolar Moment (nm): 3.84
Longitudinal (nm): 3.67
Transversal (nm): 1.14
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): 0.643543000 ± 0.000995948
Upper leaflet (nm2): 0.643543000 ± 0.000995948
Lower leaflet (nm2): 0.643543000 ± 0.000995948
Average Z coordinate
Peptide (nm): 4.8054600 ± 0.0270229
First Residue (nm): 4.8820400 ± 0.0323879
Last Residue (nm): 4.7631900 ± 0.0451295
Membrane (nm): 6.8227300 ± 0.0101734
Upper leaflet Head Group (nm): 8.7805000 ± 0.0124679
Lower leaflet Head Group (nm): 4.86330000 ± 0.00808716
Bilayer Thickness (nm): 3.9172000 ± 0.0148611
Peptide insertion (nm): 0.0578329 ± 0.0282071
Contacts
Peptide - Water: 40.300000 ± 0.781044
Peptide - Head groups: 16.172500 ± 0.281948
Peptide - Tail groups: 11.99000 ± 0.28408
Tilt (°): 92.570600 ± 0.888076
PepDF:
5(ns):  CVS
Displacement (nm): 0.6139540 ± 0.0268926
Precession(°): -0.660203 ± 1.320190
50(ns)  CVS
Displacement (nm): 1.934870 ± 0.104438
Precession(°): -6.85971 ± 4.88402
100(ns)  CVS
Displacement(nm): 2.694650 ± 0.148303
Precession(°): -15.9005 ± 7.8672
200(ns)  CVS
Displacement(nm): 4.268170 ± 0.263737
Precession(°): -33.8464 ± 11.5937

  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.