Trajectory SP836

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: P208 NC00592
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
FAKKLAKLAKKALAL
Total charge (e): +5
Number of residues: 15
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 10
  Polar: 0
Electrostatic Dipolar Moment (e nm): 4.23
Longitudinal (e nm): 3.79
Transversal (e nm): 1.89
Hydrophobic Dipolar Moment (nm): 1.84
Longitudinal (nm): 1.29
Transversal (nm): 1.31
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): 0.643712000 ± 0.000840121
Upper leaflet (nm2): 0.643712000 ± 0.000840121
Lower leaflet (nm2): 0.643712000 ± 0.000840121
Average Z coordinate
Peptide (nm): 5.1248500 ± 0.0298806
First Residue (nm): 5.1470300 ± 0.0361092
Last Residue (nm): 5.2032200 ± 0.0438281
Membrane (nm): 6.82361000 ± 0.00879796
Upper leaflet Head Group (nm): 8.7825600 ± 0.0104609
Lower leaflet Head Group (nm): 4.86218000 ± 0.00702065
Bilayer Thickness (nm): 3.9203800 ± 0.0125984
Peptide insertion (nm): -0.2626710 ± 0.0306943
Contacts
Peptide - Water: 21.015000 ± 0.688633
Peptide - Head groups: 10.545000 ± 0.224365
Peptide - Tail groups: 10.730000 ± 0.281663
Tilt (°): 94.91900 ± 1.47648
PepDF:
5(ns):  CVS
Displacement (nm): 0.7519360 ± 0.0329013
Precession(°): -1.01512 ± 2.01381
50(ns)  CVS
Displacement (nm): 2.345590 ± 0.136678
Precession(°): -10.46160 ± 5.64105
100(ns)  CVS
Displacement(nm): 3.549370 ± 0.190519
Precession(°): -21.80640 ± 8.85323
200(ns)  CVS
Displacement(nm): 4.550460 ± 0.253972
Precession(°): -36.8855 ± 12.9221

  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.