Trajectory SP1332

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: P455 AP03654
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
WLRRIKAWLRRIKA
Total charge (e): +6
Number of residues: 14
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 8
  Polar: 0
Electrostatic Dipolar Moment (e nm): 3.47
Longitudinal (e nm): 2.71
Transversal (e nm): 2.18
Hydrophobic Dipolar Moment (nm): 3.28
Longitudinal (nm): 2.92
Transversal (nm): 1.5
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): 0.6490080 ± 0.0011286
Upper leaflet (nm2): 0.6490080 ± 0.0011286
Lower leaflet (nm2): 0.6490080 ± 0.0011286
Average Z coordinate
Peptide (nm): 8.9665900 ± 0.0467756
First Residue (nm): 8.877040 ± 0.056481
Last Residue (nm): 9.2465100 ± 0.0626248
Membrane (nm): 6.8303600 ± 0.0115985
Upper leaflet Head Group (nm): 8.7712100 ± 0.0137106
Lower leaflet Head Group (nm): 4.88928000 ± 0.00949701
Bilayer Thickness (nm): 3.8819300 ± 0.0166786
Peptide insertion (nm): 0.1953770 ± 0.0487436
Contacts
Peptide - Water: 40.607500 ± 0.806845
Peptide - Head groups: 9.750000 ± 0.302619
Peptide - Tail groups: 8.455000 ± 0.289358
Tilt (°): 86.35930 ± 2.13686
PepDF:
5(ns):  CVS
Displacement (nm): 0.8342280 ± 0.0347736
Precession(°): 3.04343 ± 3.24232
50(ns)  CVS
Displacement (nm): 2.359660 ± 0.107153
Precession(°): 26.3515 ± 11.3448
100(ns)  CVS
Displacement(nm): 3.502220 ± 0.136775
Precession(°): 53.9887 ± 17.2782
200(ns)  CVS
Displacement(nm): 4.763790 ± 0.257117
Precession(°): 108.7130 ± 28.6294

  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.