Trajectory SP652

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: 19186
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P116 AP00310
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTE-
S
Total charge (e): +6
Number of residues: 36
By amino acid:
  Basic: 11
  Acidic: 5
  Hydrophobic: 15
  Polar: 5
Electrostatic Dipolar Moment (e nm): 9.47
Longitudinal (e nm): 9.43
Transversal (e nm): 0.87
Hydrophobic Dipolar Moment (nm): 2.66
Longitudinal (nm): 0.31
Transversal (nm): 2.65
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): 0.645118000 ± 0.000949658
Upper leaflet (nm2): 0.645118000 ± 0.000949658
Lower leaflet (nm2): 0.645118000 ± 0.000949658
Average Z coordinate
Peptide (nm): 8.7758800 ± 0.0317461
First Residue (nm): 8.6429300 ± 0.0464269
Last Residue (nm): 9.1857200 ± 0.0512297
Membrane (nm): 6.79397000 ± 0.00958362
Upper leaflet Head Group (nm): 8.7515700 ± 0.0114599
Lower leaflet Head Group (nm): 4.83977000 ± 0.00782352
Bilayer Thickness (nm): 3.9118000 ± 0.0138757
Peptide insertion (nm): 0.0243094 ± 0.0337512
Contacts
Peptide - Water: 55.96250 ± 0.87145
Peptide - Head groups: 20.242500 ± 0.330641
Peptide - Tail groups: 17.950000 ± 0.301925
Tilt (°): 88.359000 ± 0.763155
PepDF:
5(ns):  CVS
Displacement (nm): 0.5549530 ± 0.0233095
Precession(°): 0.685231 ± 0.993973
50(ns)  CVS
Displacement (nm): 1.6810300 ± 0.0837877
Precession(°): 4.35379 ± 3.76819
100(ns)  CVS
Displacement(nm): 2.360040 ± 0.101023
Precession(°): 3.57157 ± 5.78876
200(ns)  CVS
Displacement(nm): 3.882600 ± 0.147159
Precession(°): -0.572378 ± 8.432300

  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.