Trajectory SP916

Force field: martini_v2.2P
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: 39866
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P109 AP00013
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
LFDIIKKIAESF
Total charge (e): 0
Number of residues: 12
By amino acid:
  Basic: 2
  Acidic: 2
  Hydrophobic: 7
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.1
Longitudinal (e nm): 2.1
Transversal (e nm): 0.06
Hydrophobic Dipolar Moment (nm): 2.41
Longitudinal (nm): 1.85
Transversal (nm): 1.54
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): 0.635295000 ± 0.000953985
Upper leaflet (nm2): 0.635295000 ± 0.000953985
Lower leaflet (nm2): 0.635295000 ± 0.000953985
Average Z coordinate
Peptide (nm): 8.0692300 ± 0.0473691
First Residue (nm): 7.8801800 ± 0.0465013
Last Residue (nm): 7.9609100 ± 0.0540203
Membrane (nm): 6.05772000 ± 0.00899946
Upper leaflet Head Group (nm): 8.0537900 ± 0.0110793
Lower leaflet Head Group (nm): 4.0621400 ± 0.0073612
Bilayer Thickness (nm): 3.9916400 ± 0.0133018
Peptide insertion (nm): 0.0154441 ± 0.0486475
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 8.877500 ± 0.278792
Peptide - Tail groups: 8.182500 ± 0.232941
Tilt (°): 87.23220 ± 1.23516
PepDF:
5(ns):  CVS
Displacement (nm): 0.6550070 ± 0.0278935
Precession(°): -0.115417 ± 1.858720
50(ns)  CVS
Displacement (nm): 2.0494200 ± 0.0998354
Precession(°): -0.962003 ± 5.416030
100(ns)  CVS
Displacement(nm): 3.129360 ± 0.128534
Precession(°): -0.846772 ± 7.289950
200(ns)  CVS
Displacement(nm): 4.603310 ± 0.216064
Precession(°): -16.18720 ± 6.89162

  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.