Trajectory SP1368

Force field: martini_v3
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: 19210
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P473 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): 8.68
Longitudinal (e nm): 8.53
Transversal (e nm): 1.62
Hydrophobic Dipolar Moment (nm): 3.97
Longitudinal (nm): 3.79
Transversal (nm): 1.17
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): 0.6484680 ± 0.0011082
Upper leaflet (nm2): 0.6484680 ± 0.0011082
Lower leaflet (nm2): 0.6484680 ± 0.0011082
Average Z coordinate
Peptide (nm): 4.69244 ± 1.61753
First Residue (nm): 4.49583 ± 1.66848
Last Residue (nm): 4.91691 ± 1.60349
Membrane (nm): 6.8299200 ± 0.0124758
Upper leaflet Head Group (nm): 8.7726900 ± 0.0149593
Lower leaflet Head Group (nm): 4.88731000 ± 0.00992037
Bilayer Thickness (nm): 3.8853800 ± 0.0179498
Peptide insertion (nm): 0.194863 ± 1.617560
Contacts
Peptide - Water: 98.48000 ± 1.79634
Peptide - Head groups: 1.92000 ± 1.07582
Peptide - Tail groups: 0.0900000 ± 0.0705184
Tilt (°): 99.28610 ± 7.51304
PepDF:
5(ns):  CVS
Displacement (nm): 1.5417400 ± 0.0745253
Precession(°): 17.3569 ± 12.9943
50(ns)  CVS
Displacement (nm): 4.595090 ± 0.249637
Precession(°): 188.6100 ± 38.9656
100(ns)  CVS
Displacement(nm): 6.309730 ± 0.349441
Precession(°): 448.8590 ± 52.2154
200(ns)  CVS
Displacement(nm): 7.733750 ± 0.436377
Precession(°): 1052.1200 ± 70.4699

  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.