Trajectory SP878

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: 19191
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P229 NC02460
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
KYKKALKKLAKLL
Total charge (e): +6
Number of residues: 13
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 6
  Polar: 1
Electrostatic Dipolar Moment (e nm): 4.76
Longitudinal (e nm): 4.37
Transversal (e nm): 1.89
Hydrophobic Dipolar Moment (nm): 4.13
Longitudinal (nm): 3.93
Transversal (nm): 1.26
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): 0.64360100 ± 0.00116995
Upper leaflet (nm2): 0.64360100 ± 0.00116995
Lower leaflet (nm2): 0.64360100 ± 0.00116995
Average Z coordinate
Peptide (nm): 5.0176600 ± 0.0316013
First Residue (nm): 4.9302600 ± 0.0376124
Last Residue (nm): 5.2921500 ± 0.0483048
Membrane (nm): 6.8252000 ± 0.0124187
Upper leaflet Head Group (nm): 8.7851300 ± 0.0146354
Lower leaflet Head Group (nm): 4.8634700 ± 0.0100409
Bilayer Thickness (nm): 3.9216600 ± 0.0177486
Peptide insertion (nm): -0.1541930 ± 0.0331581
Contacts
Peptide - Water: 23.04500 ± 0.59851
Peptide - Head groups: 11.030000 ± 0.230543
Peptide - Tail groups: 9.105000 ± 0.315555
Tilt (°): 96.79260 ± 1.93646
PepDF:
5(ns):  CVS
Displacement (nm): 0.7263750 ± 0.0319971
Precession(°): -0.997545 ± 2.431510
50(ns)  CVS
Displacement (nm): 2.087990 ± 0.101972
Precession(°): -11.11830 ± 7.78875
100(ns)  CVS
Displacement(nm): 2.852160 ± 0.140803
Precession(°): -31.94240 ± 9.92569
200(ns)  CVS
Displacement(nm): 4.057680 ± 0.259344
Precession(°): -87.5629 ± 12.2922

  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.