Trajectory SP1396

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: 19209
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P487 NC01402
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
AVKQPAVVYP
Total charge (e): +1
Number of residues: 10
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 7
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.27
Longitudinal (e nm): 2.13
Transversal (e nm): 0.79
Hydrophobic Dipolar Moment (nm): 1.42
Longitudinal (nm): 1.3
Transversal (nm): 0.57
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): 0.64933800 ± 0.00109784
Upper leaflet (nm2): 0.64933800 ± 0.00109784
Lower leaflet (nm2): 0.64933800 ± 0.00109784
Average Z coordinate
Peptide (nm): 8.01078 ± 1.21990
First Residue (nm): 8.00725 ± 1.22398
Last Residue (nm): 8.05146 ± 1.25598
Membrane (nm): 6.8325600 ± 0.0115616
Upper leaflet Head Group (nm): 8.7736900 ± 0.0137876
Lower leaflet Head Group (nm): 4.89077000 ± 0.00950069
Bilayer Thickness (nm): 3.882920 ± 0.016744
Peptide insertion (nm): -0.762916 ± 1.219980
Contacts
Peptide - Water: 25.94000 ± 4.39779
Peptide - Head groups: 6.42750 ± 1.27248
Peptide - Tail groups: 5.5025 ± 1.2113
Tilt (°): 90.29240 ± 3.59207
PepDF:
5(ns):  CVS
Displacement (nm): 1.2169700 ± 0.0779134
Precession(°): 1.05615 ± 11.42810
50(ns)  CVS
Displacement (nm): 3.631310 ± 0.166712
Precession(°): 26.8926 ± 40.5056
100(ns)  CVS
Displacement(nm): 4.966260 ± 0.242512
Precession(°): 56.3297 ± 57.8345
200(ns)  CVS
Displacement(nm): 8.399480 ± 0.399325
Precession(°): 192.3090 ± 72.3699

  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.