Trajectory SP856

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: 19194
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P218 NC01800
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
KITLKLAIKAWKLALKAA
Total charge (e): +5
Number of residues: 18
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 12
  Polar: 1
Electrostatic Dipolar Moment (e nm): 5.09
Longitudinal (e nm): 4.61
Transversal (e nm): 2.17
Hydrophobic Dipolar Moment (nm): 0.98
Longitudinal (nm): 0.6
Transversal (nm): 0.77
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): 0.64317100 ± 0.00103771
Upper leaflet (nm2): 0.64317100 ± 0.00103771
Lower leaflet (nm2): 0.64317100 ± 0.00103771
Average Z coordinate
Peptide (nm): 8.6424300 ± 0.0309281
First Residue (nm): 8.6407100 ± 0.0382437
Last Residue (nm): 8.6577300 ± 0.0477409
Membrane (nm): 6.828150 ± 0.010925
Upper leaflet Head Group (nm): 8.7895700 ± 0.0131485
Lower leaflet Head Group (nm): 4.86828000 ± 0.00858975
Bilayer Thickness (nm): 3.9213000 ± 0.0157057
Peptide insertion (nm): -0.1471440 ± 0.0336071
Contacts
Peptide - Water: 24.370000 ± 0.742119
Peptide - Head groups: 12.88000 ± 0.24258
Peptide - Tail groups: 10.442500 ± 0.238967
Tilt (°): 87.32140 ± 1.10907
PepDF:
5(ns):  CVS
Displacement (nm): 0.6624270 ± 0.0282577
Precession(°): 3.55150 ± 1.73729
50(ns)  CVS
Displacement (nm): 1.7889700 ± 0.0901883
Precession(°): 29.96600 ± 5.96245
100(ns)  CVS
Displacement(nm): 2.594210 ± 0.108571
Precession(°): 54.58960 ± 9.00937
200(ns)  CVS
Displacement(nm): 3.927940 ± 0.136836
Precession(°): 109.0760 ± 11.5989

  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.