Trajectory SP933

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: 45448
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P256 AP00414
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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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): 6.58
Longitudinal (e nm): 6.17
Transversal (e nm): 2.28
Hydrophobic Dipolar Moment (nm): 3.52
Longitudinal (nm): 3.07
Transversal (nm): 1.74
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): 0.651008000 ± 0.000919091
Upper leaflet (nm2): 0.651008000 ± 0.000919091
Lower leaflet (nm2): 0.651008000 ± 0.000919091
Average Z coordinate
Peptide (nm): 4.7960200 ± 0.0337913
First Residue (nm): 4.7559800 ± 0.0466304
Last Residue (nm): 4.7354700 ± 0.0571063
Membrane (nm): 6.55418000 ± 0.00923535
Upper leaflet Head Group (nm): 8.5184200 ± 0.0110157
Lower leaflet Head Group (nm): 4.5863300 ± 0.0075867
Bilayer Thickness (nm): 3.9320900 ± 0.0133755
Peptide insertion (nm): -0.2096850 ± 0.0346325
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 15.005000 ± 0.282666
Peptide - Tail groups: 15.457500 ± 0.274196
Tilt (°): 92.5872 ± 1.1357
PepDF:
5(ns):  CVS
Displacement (nm): 0.5735270 ± 0.0246333
Precession(°): 1.445020 ± 0.985558
50(ns)  CVS
Displacement (nm): 1.7851700 ± 0.0929004
Precession(°): 14.14280 ± 2.40426
100(ns)  CVS
Displacement(nm): 2.514770 ± 0.150754
Precession(°): 29.47210 ± 3.45249
200(ns)  CVS
Displacement(nm): 3.82871 ± 0.24458
Precession(°): 66.59520 ± 3.24284

  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.