Trajectory SP864

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: 19191
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P222 NC02053
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
STNITVTLKKFPL
Total charge (e): +2
Number of residues: 13
By amino acid:
  Basic: 2
  Acidic: 0
  Hydrophobic: 6
  Polar: 5
Electrostatic Dipolar Moment (e nm): 1.88
Longitudinal (e nm): 1.71
Transversal (e nm): 0.78
Hydrophobic Dipolar Moment (nm): 1.97
Longitudinal (nm): 1.74
Transversal (nm): 0.92
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
 
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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): 0.642809000 ± 0.000975431
Upper leaflet (nm2): 0.642809000 ± 0.000975431
Lower leaflet (nm2): 0.642809000 ± 0.000975431
Average Z coordinate
Peptide (nm): 8.575220 ± 0.035524
First Residue (nm): 8.769360 ± 0.035531
Last Residue (nm): 8.4786300 ± 0.0499767
Membrane (nm): 6.8307800 ± 0.0101883
Upper leaflet Head Group (nm): 8.7931900 ± 0.0120157
Lower leaflet Head Group (nm): 4.87103000 ± 0.00810795
Bilayer Thickness (nm): 3.9221600 ± 0.0144954
Peptide insertion (nm): -0.2179710 ± 0.0375011
Contacts
Peptide - Water: 18.972500 ± 0.497512
Peptide - Head groups: 9.525000 ± 0.234524
Peptide - Tail groups: 9.247500 ± 0.221798
Tilt (°): 104.50000 ± 1.51595
PepDF:
5(ns):  CVS
Displacement (nm): 0.7408130 ± 0.0307003
Precession(°): 2.68814 ± 2.75787
50(ns)  CVS
Displacement (nm): 2.23787 ± 0.13320
Precession(°): 27.31560 ± 8.99438
100(ns)  CVS
Displacement(nm): 3.562680 ± 0.163025
Precession(°): 60.6587 ± 11.4477
200(ns)  CVS
Displacement(nm): 4.76007 ± 0.21593
Precession(°): 136.4790 ± 12.6386

  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.