Trajectory SP1344

Force field: martini_v3
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: 19204
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P461 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): 6.57
Longitudinal (e nm): 5.9
Transversal (e nm): 2.9
Hydrophobic Dipolar Moment (nm): 3.31
Longitudinal (nm): 2.45
Transversal (nm): 2.21
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)
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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): 0.649398 ± 0.001181
Upper leaflet (nm2): 0.649398 ± 0.001181
Lower leaflet (nm2): 0.649398 ± 0.001181
Average Z coordinate
Peptide (nm): 9.0789700 ± 0.0388947
First Residue (nm): 8.9775400 ± 0.0477699
Last Residue (nm): 9.1180600 ± 0.0528285
Membrane (nm): 6.8200700 ± 0.0121902
Upper leaflet Head Group (nm): 8.7596400 ± 0.0147221
Lower leaflet Head Group (nm): 4.88053000 ± 0.00971236
Bilayer Thickness (nm): 3.8791200 ± 0.0176372
Peptide insertion (nm): 0.3193270 ± 0.0415877
Contacts
Peptide - Water: 56.41250 ± 1.04642
Peptide - Head groups: 10.995000 ± 0.269421
Peptide - Tail groups: 8.577500 ± 0.277649
Tilt (°): 88.85820 ± 1.42196
PepDF:
5(ns):  CVS
Displacement (nm): 0.8035120 ± 0.0363386
Precession(°): -1.83948 ± 2.48761
50(ns)  CVS
Displacement (nm): 2.399490 ± 0.117843
Precession(°): -21.63850 ± 7.76751
100(ns)  CVS
Displacement(nm): 3.267020 ± 0.165784
Precession(°): -47.1535 ± 12.2116
200(ns)  CVS
Displacement(nm): 4.672820 ± 0.193685
Precession(°): -116.7240 ± 19.1691

  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.