Trajectory SP810

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: 19196
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P195 AP04269
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
ILGKLWKGVKSIF
Total charge (e): +3
Number of residues: 13
By amino acid:
  Basic: 3
  Acidic: 0
  Hydrophobic: 9
  Polar: 1
Electrostatic Dipolar Moment (e nm): 3.35
Longitudinal (e nm): 2.98
Transversal (e nm): 1.52
Hydrophobic Dipolar Moment (nm): 1.59
Longitudinal (nm): 0.49
Transversal (nm): 1.51
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): 0.64361300 ± 0.00110987
Upper leaflet (nm2): 0.64361300 ± 0.00110987
Lower leaflet (nm2): 0.64361300 ± 0.00110987
Average Z coordinate
Peptide (nm): 8.5641000 ± 0.0396347
First Residue (nm): 8.4134300 ± 0.0471568
Last Residue (nm): 8.6012300 ± 0.0476707
Membrane (nm): 6.8247100 ± 0.0111474
Upper leaflet Head Group (nm): 8.7851600 ± 0.0130908
Lower leaflet Head Group (nm): 4.86508000 ± 0.00926364
Bilayer Thickness (nm): 3.920070 ± 0.016037
Peptide insertion (nm): -0.2210550 ± 0.0417406
Contacts
Peptide - Water: 19.070000 ± 0.566841
Peptide - Head groups: 10.042500 ± 0.240023
Peptide - Tail groups: 9.960000 ± 0.278686
Tilt (°): 84.95400 ± 1.60846
PepDF:
5(ns):  CVS
Displacement (nm): 0.7495430 ± 0.0317925
Precession(°): 0.216899 ± 2.629650
50(ns)  CVS
Displacement (nm): 2.401860 ± 0.116537
Precession(°): 1.46415 ± 7.76594
100(ns)  CVS
Displacement(nm): 3.263480 ± 0.178792
Precession(°): -4.07726 ± 11.51910
200(ns)  CVS
Displacement(nm): 3.205860 ± 0.177439
Precession(°): -34.4521 ± 19.4570

  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.