Trajectory SP752

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: 19192
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P166 AP03112
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LSLLLSLGLKLL
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 9
  Polar: 2
Electrostatic Dipolar Moment (e nm): 1.62
Longitudinal (e nm): 1.49
Transversal (e nm): 0.64
Hydrophobic Dipolar Moment (nm): 0.85
Longitudinal (nm): 0.61
Transversal (nm): 0.6
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): 0.64279500 ± 0.00106446
Upper leaflet (nm2): 0.64279500 ± 0.00106446
Lower leaflet (nm2): 0.64279500 ± 0.00106446
Average Z coordinate
Peptide (nm): 5.2490400 ± 0.0325753
First Residue (nm): 5.2059300 ± 0.0377639
Last Residue (nm): 5.2278000 ± 0.0419463
Membrane (nm): 6.8352100 ± 0.0112666
Upper leaflet Head Group (nm): 8.7959500 ± 0.0134024
Lower leaflet Head Group (nm): 4.87240000 ± 0.00900021
Bilayer Thickness (nm): 3.923550 ± 0.016144
Peptide insertion (nm): -0.3766370 ± 0.0337957
Contacts
Peptide - Water: 13.342500 ± 0.530273
Peptide - Head groups: 8.402500 ± 0.240953
Peptide - Tail groups: 9.530000 ± 0.226335
Tilt (°): 91.75100 ± 1.61093
PepDF:
5(ns):  CVS
Displacement (nm): 0.7630930 ± 0.0319492
Precession(°): 3.52406 ± 3.12768
50(ns)  CVS
Displacement (nm): 2.272390 ± 0.119894
Precession(°): 42.16070 ± 9.81394
100(ns)  CVS
Displacement(nm): 2.852900 ± 0.145099
Precession(°): 83.5317 ± 13.6836
200(ns)  CVS
Displacement(nm): 2.759700 ± 0.137557
Precession(°): 161.5760 ± 13.7535

  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.