Trajectory SP1208

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: 19212
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P393 AP00414
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
IGSALKKALPVAKKIGKIALPIAKAALP
Total charge (e): +6
Number of residues: 28
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 21
  Polar: 1
Electrostatic Dipolar Moment (e nm): 7.65
Longitudinal (e nm): 7.13
Transversal (e nm): 2.77
Hydrophobic Dipolar Moment (nm): 3.53
Longitudinal (nm): 3.08
Transversal (nm): 1.73
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): 0.65101800 ± 0.00101125
Upper leaflet (nm2): 0.65101800 ± 0.00101125
Lower leaflet (nm2): 0.65101800 ± 0.00101125
Average Z coordinate
Peptide (nm): 4.818030 ± 0.034238
First Residue (nm): 4.845990 ± 0.044541
Last Residue (nm): 4.7489700 ± 0.0524239
Membrane (nm): 6.8062700 ± 0.0104849
Upper leaflet Head Group (nm): 8.7414600 ± 0.0128262
Lower leaflet Head Group (nm): 4.86928000 ± 0.00853042
Bilayer Thickness (nm): 3.8721700 ± 0.0154039
Peptide insertion (nm): 0.0512496 ± 0.0352847
Contacts
Peptide - Water: 48.045000 ± 0.754603
Peptide - Head groups: 13.650000 ± 0.273405
Peptide - Tail groups: 13.702500 ± 0.252239
Tilt (°): 92.76280 ± 1.05038
PepDF:
5(ns):  CVS
Displacement (nm): 0.7291470 ± 0.0309797
Precession(°): -0.791918 ± 1.437700
50(ns)  CVS
Displacement (nm): 2.403510 ± 0.134726
Precession(°): -5.68068 ± 5.73757
100(ns)  CVS
Displacement(nm): 4.012110 ± 0.222835
Precession(°): -6.59827 ± 8.75891
200(ns)  CVS
Displacement(nm): 6.630020 ± 0.361266
Precession(°): -16.3600 ± 10.0857

  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.