Trajectory SP794

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: 19189
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P187 AP03756
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
RFKRFRKKFKKLFKKLS
Total charge (e): +10
Number of residues: 17
By amino acid:
  Basic: 10
  Acidic: 0
  Hydrophobic: 6
  Polar: 1
Electrostatic Dipolar Moment (e nm): 6.58
Longitudinal (e nm): 5.91
Transversal (e nm): 2.9
Hydrophobic Dipolar Moment (nm): 3.32
Longitudinal (nm): 2.5
Transversal (nm): 2.19
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): 0.643692000 ± 0.000908461
Upper leaflet (nm2): 0.643692000 ± 0.000908461
Lower leaflet (nm2): 0.643692000 ± 0.000908461
Average Z coordinate
Peptide (nm): 4.8875700 ± 0.0321158
First Residue (nm): 4.8578300 ± 0.0444904
Last Residue (nm): 5.0096600 ± 0.0450579
Membrane (nm): 6.82027000 ± 0.00963838
Upper leaflet Head Group (nm): 8.7785600 ± 0.0116933
Lower leaflet Head Group (nm): 4.85896000 ± 0.00760159
Bilayer Thickness (nm): 3.9196000 ± 0.0139469
Peptide insertion (nm): -0.0286175 ± 0.0330032
Contacts
Peptide - Water: 35.775000 ± 0.827135
Peptide - Head groups: 14.082500 ± 0.302331
Peptide - Tail groups: 10.840000 ± 0.306892
Tilt (°): 96.30650 ± 1.28958
PepDF:
5(ns):  CVS
Displacement (nm): 0.690189 ± 0.029449
Precession(°): 2.29449 ± 1.81975
50(ns)  CVS
Displacement (nm): 2.196570 ± 0.102198
Precession(°): 22.1726 ± 5.5530
100(ns)  CVS
Displacement(nm): 2.916600 ± 0.150231
Precession(°): 43.45240 ± 8.08577
200(ns)  CVS
Displacement(nm): 3.732690 ± 0.210607
Precession(°): 74.23680 ± 9.60173

  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.