Trajectory SP1238

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: P408 AP01019
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
ETFDKLKEKLKTFYQKLVEKAEDLKGDLKAKLS
Total charge (e): +2
Number of residues: 33
By amino acid:
  Basic: 9
  Acidic: 7
  Hydrophobic: 12
  Polar: 5
Electrostatic Dipolar Moment (e nm): 4.57
Longitudinal (e nm): 4.3
Transversal (e nm): 1.57
Hydrophobic Dipolar Moment (nm): 2.28
Longitudinal (nm): 0.12
Transversal (nm): 2.28
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): 0.65009400 ± 0.00117327
Upper leaflet (nm2): 0.65009400 ± 0.00117327
Lower leaflet (nm2): 0.65009400 ± 0.00117327
Average Z coordinate
Peptide (nm): 4.5377300 ± 0.0292572
First Residue (nm): 4.3363800 ± 0.0444898
Last Residue (nm): 4.4266300 ± 0.0431797
Membrane (nm): 6.8118800 ± 0.0125591
Upper leaflet Head Group (nm): 8.7488700 ± 0.0149396
Lower leaflet Head Group (nm): 4.87666000 ± 0.00986456
Bilayer Thickness (nm): 3.8722100 ± 0.0179025
Peptide insertion (nm): 0.3389320 ± 0.0308755
Contacts
Peptide - Water: 71.45000 ± 1.25676
Peptide - Head groups: 16.375000 ± 0.363586
Peptide - Tail groups: 13.720000 ± 0.404846
Tilt (°): 90.578000 ± 0.757875
PepDF:
5(ns):  CVS
Displacement (nm): 0.6857680 ± 0.0273074
Precession(°): 0.390938 ± 1.190680
50(ns)  CVS
Displacement (nm): 2.074080 ± 0.093612
Precession(°): 3.10641 ± 3.66728
100(ns)  CVS
Displacement(nm): 3.168320 ± 0.149898
Precession(°): 4.62250 ± 4.81664
200(ns)  CVS
Displacement(nm): 5.01506 ± 0.24125
Precession(°): 4.39982 ± 5.69734

  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.