Trajectory SP702

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: 19197
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P141 AP01623
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
FKLKGMARISCLPNGQWSNFPPKCIRECAMVSS
Total charge (e): +4
Number of residues: 33
By amino acid:
  Basic: 5
  Acidic: 1
  Hydrophobic: 17
  Polar: 10
Electrostatic Dipolar Moment (e nm): 11.64
Longitudinal (e nm): 11.45
Transversal (e nm): 2.09
Hydrophobic Dipolar Moment (nm): 1.48
Longitudinal (nm): 0.31
Transversal (nm): 1.45
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)
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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): 0.645573000 ± 0.000957373
Upper leaflet (nm2): 0.645573000 ± 0.000957373
Lower leaflet (nm2): 0.645573000 ± 0.000957373
Average Z coordinate
Peptide (nm): 8.6594300 ± 0.0342633
First Residue (nm): 8.6643000 ± 0.0460284
Last Residue (nm): 8.886110 ± 0.049997
Membrane (nm): 6.79883000 ± 0.00990732
Upper leaflet Head Group (nm): 8.7566400 ± 0.0115765
Lower leaflet Head Group (nm): 4.84422000 ± 0.00811059
Bilayer Thickness (nm): 3.912420 ± 0.014135
Peptide insertion (nm): -0.0972091 ± 0.0361662
Contacts
Peptide - Water: 43.71500 ± 1.01896
Peptide - Head groups: 19.165000 ± 0.297678
Peptide - Tail groups: 17.950000 ± 0.286354
Tilt (°): 90.028200 ± 0.788753
PepDF:
5(ns):  CVS
Displacement (nm): 0.5734550 ± 0.0230851
Precession(°): 1.255860 ± 0.961949
50(ns)  CVS
Displacement (nm): 1.4881300 ± 0.0766489
Precession(°): 11.84840 ± 3.55303
100(ns)  CVS
Displacement(nm): 2.081880 ± 0.109526
Precession(°): 22.8030 ± 5.1857
200(ns)  CVS
Displacement(nm): 2.789580 ± 0.142741
Precession(°): 53.73470 ± 6.68876

  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.