Trajectory SP1009

Force field: martini_v2.2P
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: 45476
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P294 AP02872
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
IFSKLAGKKIKNLLISGLKG
Total charge (e): +5
Number of residues: 20
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 12
  Polar: 3
Electrostatic Dipolar Moment (e nm): 4.43
Longitudinal (e nm): 4.25
Transversal (e nm): 1.26
Hydrophobic Dipolar Moment (nm): 1.99
Longitudinal (nm): 1.93
Transversal (nm): 0.5
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): 0.64950500 ± 0.00101225
Upper leaflet (nm2): 0.64950500 ± 0.00101225
Lower leaflet (nm2): 0.64950500 ± 0.00101225
Average Z coordinate
Peptide (nm): 4.7558500 ± 0.0335079
First Residue (nm): 4.733580 ± 0.043738
Last Residue (nm): 4.6247700 ± 0.0475743
Membrane (nm): 6.5701000 ± 0.0101763
Upper leaflet Head Group (nm): 8.5377100 ± 0.0121458
Lower leaflet Head Group (nm): 4.60032000 ± 0.00829376
Bilayer Thickness (nm): 3.9374000 ± 0.0147074
Peptide insertion (nm): -0.155534 ± 0.034519
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 12.860000 ± 0.318492
Peptide - Tail groups: 12.020000 ± 0.311357
Tilt (°): 86.81220 ± 1.25003
PepDF:
5(ns):  CVS
Displacement (nm): 0.6249960 ± 0.0255236
Precession(°): 0.0671446 ± 1.3202700
50(ns)  CVS
Displacement (nm): 1.8314000 ± 0.0938698
Precession(°): -0.947277 ± 3.907810
100(ns)  CVS
Displacement(nm): 2.481000 ± 0.133279
Precession(°): -3.64525 ± 5.47766
200(ns)  CVS
Displacement(nm): 3.663530 ± 0.143205
Precession(°): -11.46630 ± 6.81956

  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.