Trajectory SP716

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: 19189
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P148 AP02162
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
IKIPWGKVKDFLVGGMKAV
Total charge (e): +3
Number of residues: 19
By amino acid:
  Basic: 4
  Acidic: 1
  Hydrophobic: 14
  Polar: 0
Electrostatic Dipolar Moment (e nm): 4.49
Longitudinal (e nm): 4.39
Transversal (e nm): 0.9
Hydrophobic Dipolar Moment (nm): 2.35
Longitudinal (nm): 2.02
Transversal (nm): 1.19
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): 0.644205000 ± 0.000988488
Upper leaflet (nm2): 0.644205000 ± 0.000988488
Lower leaflet (nm2): 0.644205000 ± 0.000988488
Average Z coordinate
Peptide (nm): 8.5312400 ± 0.0365957
First Residue (nm): 8.4221800 ± 0.0439108
Last Residue (nm): 8.5240700 ± 0.0482247
Membrane (nm): 6.813320 ± 0.010142
Upper leaflet Head Group (nm): 8.7746700 ± 0.0123317
Lower leaflet Head Group (nm): 4.85518000 ± 0.00794059
Bilayer Thickness (nm): 3.9194900 ± 0.0146671
Peptide insertion (nm): -0.2434350 ± 0.0386175
Contacts
Peptide - Water: 25.402500 ± 0.548941
Peptide - Head groups: 12.182500 ± 0.278524
Peptide - Tail groups: 12.442500 ± 0.318856
Tilt (°): 86.66320 ± 1.14526
PepDF:
5(ns):  CVS
Displacement (nm): 0.6568280 ± 0.0263843
Precession(°): 0.347751 ± 1.769620
50(ns)  CVS
Displacement (nm): 1.5834500 ± 0.0783749
Precession(°): 3.57806 ± 6.17884
100(ns)  CVS
Displacement(nm): 1.9120700 ± 0.0840314
Precession(°): 4.50850 ± 9.53689
200(ns)  CVS
Displacement(nm): 2.572710 ± 0.140667
Precession(°): -3.86324 ± 14.24370

  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.