Trajectory SP1222

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: 19208
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P400 AP00952
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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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): 5.72
Longitudinal (e nm): 4.42
Transversal (e nm): 3.64
Hydrophobic Dipolar Moment (nm): 2.84
Longitudinal (nm): 1.48
Transversal (nm): 2.42
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): 0.649395000 ± 0.000977938
Upper leaflet (nm2): 0.649395000 ± 0.000977938
Lower leaflet (nm2): 0.649395000 ± 0.000977938
Average Z coordinate
Peptide (nm): 4.6621500 ± 0.0342461
First Residue (nm): 4.8320300 ± 0.0472012
Last Residue (nm): 4.4123600 ± 0.0523781
Membrane (nm): 6.82042000 ± 0.00960166
Upper leaflet Head Group (nm): 8.7598200 ± 0.0116079
Lower leaflet Head Group (nm): 4.88151000 ± 0.00769375
Bilayer Thickness (nm): 3.8783200 ± 0.0139261
Peptide insertion (nm): 0.2193560 ± 0.0350997
Contacts
Peptide - Water: 55.28500 ± 1.03098
Peptide - Head groups: 12.020000 ± 0.306995
Peptide - Tail groups: 10.362500 ± 0.229191
Tilt (°): 86.0121 ± 1.3184
PepDF:
5(ns):  CVS
Displacement (nm): 0.7642130 ± 0.0318292
Precession(°): 2.58763 ± 1.96261
50(ns)  CVS
Displacement (nm): 2.62968 ± 0.11920
Precession(°): 30.81930 ± 6.81647
100(ns)  CVS
Displacement(nm): 4.039750 ± 0.164062
Precession(°): 72.49950 ± 8.71759
200(ns)  CVS
Displacement(nm): 6.805900 ± 0.251251
Precession(°): 155.66600 ± 9.82624

  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.