Trajectory SP714

Force field: martini_v2.2
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: 19186
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P147 AP02151
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LYKKLLKKLLKSAKKLG
Total charge (e): +7
Number of residues: 17
By amino acid:
  Basic: 7
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 4.62
Longitudinal (e nm): 3.85
Transversal (e nm): 2.56
Hydrophobic Dipolar Moment (nm): 3.19
Longitudinal (nm): 2.63
Transversal (nm): 1.82
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
 
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Contacts per residue
(normalized by number of beads in the residue)
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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): 0.643337000 ± 0.000955442
Upper leaflet (nm2): 0.643337000 ± 0.000955442
Lower leaflet (nm2): 0.643337000 ± 0.000955442
Average Z coordinate
Peptide (nm): 8.6531300 ± 0.0319322
First Residue (nm): 8.442350 ± 0.041539
Last Residue (nm): 8.7085300 ± 0.0447933
Membrane (nm): 6.82282000 ± 0.00986939
Upper leaflet Head Group (nm): 8.7846700 ± 0.0116337
Lower leaflet Head Group (nm): 4.86350000 ± 0.00800855
Bilayer Thickness (nm): 3.9211700 ± 0.0141237
Peptide insertion (nm): -0.1315320 ± 0.0339854
Contacts
Peptide - Water: 27.937500 ± 0.708152
Peptide - Head groups: 12.002500 ± 0.228057
Peptide - Tail groups: 10.752500 ± 0.224099
Tilt (°): 84.0294 ± 1.2411
PepDF:
5(ns):  CVS
Displacement (nm): 0.6704410 ± 0.0299395
Precession(°): 2.83700 ± 1.88986
50(ns)  CVS
Displacement (nm): 1.701360 ± 0.107236
Precession(°): 27.08930 ± 6.40184
100(ns)  CVS
Displacement(nm): 2.39191 ± 0.14417
Precession(°): 49.67090 ± 9.35559
200(ns)  CVS
Displacement(nm): 3.46941 ± 0.20470
Precession(°): 81.7501 ± 15.3400

  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.