Trajectory SP886

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: P233 NC02629
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
KTVLLRKLLKLLVRKI
Total charge (e): +6
Number of residues: 16
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 9
  Polar: 1
Electrostatic Dipolar Moment (e nm): 4.02
Longitudinal (e nm): 3.86
Transversal (e nm): 1.11
Hydrophobic Dipolar Moment (nm): 1.27
Longitudinal (nm): 0.79
Transversal (nm): 1
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): 0.643599000 ± 0.000914528
Upper leaflet (nm2): 0.643599000 ± 0.000914528
Lower leaflet (nm2): 0.643599000 ± 0.000914528
Average Z coordinate
Peptide (nm): 8.6383300 ± 0.0407025
First Residue (nm): 8.594460 ± 0.047007
Last Residue (nm): 8.3961800 ± 0.0472696
Membrane (nm): 6.82418000 ± 0.00949894
Upper leaflet Head Group (nm): 8.7861300 ± 0.0111988
Lower leaflet Head Group (nm): 4.86474000 ± 0.00820227
Bilayer Thickness (nm): 3.9213900 ± 0.0138813
Peptide insertion (nm): -0.147803 ± 0.042215
Contacts
Peptide - Water: 25.692500 ± 0.563113
Peptide - Head groups: 12.140000 ± 0.212676
Peptide - Tail groups: 9.837500 ± 0.266791
Tilt (°): 95.43980 ± 1.23868
PepDF:
5(ns):  CVS
Displacement (nm): 0.7029680 ± 0.0292136
Precession(°): -0.199938 ± 1.961400
50(ns)  CVS
Displacement (nm): 1.97106 ± 0.10778
Precession(°): -6.24645 ± 5.35121
100(ns)  CVS
Displacement(nm): 3.16212 ± 0.16654
Precession(°): -9.59910 ± 7.08767
200(ns)  CVS
Displacement(nm): 4.706240 ± 0.219804
Precession(°): -30.25300 ± 9.11751

  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.