Trajectory SP1365

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: 17403
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P471 AP04628
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
RRLSKVLGKLRDKIATWRQRLLTK
Total charge (e): +8
Number of residues: 24
By amino acid:
  Basic: 9
  Acidic: 1
  Hydrophobic: 10
  Polar: 4
Electrostatic Dipolar Moment (e nm): 8
Longitudinal (e nm): 7.96
Transversal (e nm): 0.79
Hydrophobic Dipolar Moment (nm): 3.59
Longitudinal (nm): 3.19
Transversal (nm): 1.66
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: POPG:POPE (1:3) (Gram-negative bacteria)

POPE
1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Total charge (e): 0

  See POPE lipid
  Download ITP File.
  Download PDB File.
POPG
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Total charge (e): -1

  See POPG 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): 0.614428000 ± 0.000982263
Upper leaflet (nm2): 0.614428000 ± 0.000982263
Lower leaflet (nm2): 0.614428000 ± 0.000982263
Average Z coordinate
Peptide (nm): 8.6216500 ± 0.0405572
First Residue (nm): 8.6751300 ± 0.0572848
Last Residue (nm): 8.8630600 ± 0.0626174
Membrane (nm): 6.3993300 ± 0.0100717
Upper leaflet Head Group (nm): 8.4118100 ± 0.0121057
Lower leaflet Head Group (nm): 4.38685000 ± 0.00820039
Bilayer Thickness (nm): 4.0249600 ± 0.0146217
Peptide insertion (nm): 0.2098410 ± 0.0423253
Contacts
Peptide - Water: 53.8225 ± 1.1206
Peptide - Head groups: 15.175000 ± 0.338805
Peptide - Tail groups: 11.792500 ± 0.266056
Tilt (°): 84.4329 ± 1.3888
PepDF:
5(ns):  CVS
Displacement (nm): 0.6452640 ± 0.0264275
Precession(°): 0.0898275 ± 1.4864000
50(ns)  CVS
Displacement (nm): 1.7208200 ± 0.0822219
Precession(°): -0.147926 ± 3.497940
100(ns)  CVS
Displacement(nm): 2.181990 ± 0.121929
Precession(°): 1.56843 ± 4.44899
200(ns)  CVS
Displacement(nm): 3.017210 ± 0.170769
Precession(°): 11.4101 ± 5.7821

  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.