Trajectory SP1426

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: 19206
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P502 NC02437
Lipids: POPC
Heteromolecules:
Ions:
Water model: W

  Download all Compresed Files.


Sequence :
GFPGTPGLPGF
Total charge (e): 0
Number of residues: 11
By amino acid:
  Basic: 0
  Acidic: 0
  Hydrophobic: 10
  Polar: 1
Electrostatic Dipolar Moment (e nm): 1.67
Longitudinal (e nm): 1.67
Transversal (e nm): 0
Hydrophobic Dipolar Moment (nm): 0.88
Longitudinal (nm): 0.81
Transversal (nm): 0.35
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): 0.649093000 ± 0.000977559
Upper leaflet (nm2): 0.649093000 ± 0.000977559
Lower leaflet (nm2): 0.649093000 ± 0.000977559
Average Z coordinate
Peptide (nm): 8.6405000 ± 0.0430442
First Residue (nm): 8.8445700 ± 0.0464032
Last Residue (nm): 8.8289300 ± 0.0537947
Membrane (nm): 6.83496 ± 0.01013
Upper leaflet Head Group (nm): 8.7768500 ± 0.0120475
Lower leaflet Head Group (nm): 4.89312000 ± 0.00809684
Bilayer Thickness (nm): 3.8837300 ± 0.0145155
Peptide insertion (nm): -0.1363540 ± 0.0446984
Contacts
Peptide - Water: 17.265000 ± 0.623526
Peptide - Head groups: 7.737500 ± 0.235077
Peptide - Tail groups: 7.910000 ± 0.270231
Tilt (°): 91.47170 ± 2.09676
PepDF:
5(ns):  CVS
Displacement (nm): 0.9928890 ± 0.0429685
Precession(°): -0.229603 ± 5.148680
50(ns)  CVS
Displacement (nm): 3.110010 ± 0.174407
Precession(°): -1.81521 ± 15.84690
100(ns)  CVS
Displacement(nm): 4.36835 ± 0.30928
Precession(°): -13.2663 ± 23.8341
200(ns)  CVS
Displacement(nm): 7.80384 ± 0.40764
Precession(°): -53.5977 ± 31.9585

  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.