Trajectory SP947

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: 45467
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P263 AP00952
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
IGKFLKKAKKFGKAFVKILKK
Total charge (e): +9
Number of residues: 21
By amino acid:
  Basic: 9
  Acidic: 0
  Hydrophobic: 12
  Polar: 0
Electrostatic Dipolar Moment (e nm): 5.17
Longitudinal (e nm): 4.16
Transversal (e nm): 3.06
Hydrophobic Dipolar Moment (nm): 2.87
Longitudinal (nm): 1.45
Transversal (nm): 2.47
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): 0.649584000 ± 0.000939413
Upper leaflet (nm2): 0.649584000 ± 0.000939413
Lower leaflet (nm2): 0.649584000 ± 0.000939413
Average Z coordinate
Peptide (nm): 4.592920 ± 0.029883
First Residue (nm): 4.7097800 ± 0.0397456
Last Residue (nm): 4.4304700 ± 0.0366344
Membrane (nm): 6.5689500 ± 0.0093211
Upper leaflet Head Group (nm): 8.5364800 ± 0.0110901
Lower leaflet Head Group (nm): 4.60038000 ± 0.00747962
Bilayer Thickness (nm): 3.9361000 ± 0.0133767
Peptide insertion (nm): 0.00745458 ± 0.03080480
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 13.780000 ± 0.254508
Peptide - Tail groups: 12.292500 ± 0.287189
Tilt (°): 89.521200 ± 0.921662
PepDF:
5(ns):  CVS
Displacement (nm): 0.6098340 ± 0.0252391
Precession(°): -0.0824854 ± 1.2183500
50(ns)  CVS
Displacement (nm): 1.9759300 ± 0.0933144
Precession(°): -2.22476 ± 3.63501
100(ns)  CVS
Displacement(nm): 2.813140 ± 0.141139
Precession(°): -7.59670 ± 4.84959
200(ns)  CVS
Displacement(nm): 4.574230 ± 0.250712
Precession(°): -22.87180 ± 5.24299

  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.