Trajectory SP1010

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: 39859
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P294 AP02872
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
IFSKLAGKKIKNLLISGLKG
Total charge (e): +5
Number of residues: 20
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 12
  Polar: 3
Electrostatic Dipolar Moment (e nm): 4.43
Longitudinal (e nm): 4.25
Transversal (e nm): 1.26
Hydrophobic Dipolar Moment (nm): 1.99
Longitudinal (nm): 1.93
Transversal (nm): 0.5
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): 0.636122000 ± 0.000976911
Upper leaflet (nm2): 0.636122000 ± 0.000976911
Lower leaflet (nm2): 0.636122000 ± 0.000976911
Average Z coordinate
Peptide (nm): 7.8640600 ± 0.0385327
First Residue (nm): 7.9009700 ± 0.0556233
Last Residue (nm): 8.0019600 ± 0.0410323
Membrane (nm): 6.04792000 ± 0.00947628
Upper leaflet Head Group (nm): 8.0437300 ± 0.0112962
Lower leaflet Head Group (nm): 4.05397000 ± 0.00742359
Bilayer Thickness (nm): 3.9897600 ± 0.0135171
Peptide insertion (nm): -0.1796730 ± 0.0401543
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 13.042500 ± 0.287786
Peptide - Tail groups: 12.155000 ± 0.328834
Tilt (°): 87.07740 ± 1.25927
PepDF:
5(ns):  CVS
Displacement (nm): 0.5492790 ± 0.0223154
Precession(°): 1.05144 ± 1.27023
50(ns)  CVS
Displacement (nm): 1.5092000 ± 0.0714856
Precession(°): 11.4245 ± 4.1121
100(ns)  CVS
Displacement(nm): 2.093790 ± 0.101119
Precession(°): 25.26050 ± 4.26357
200(ns)  CVS
Displacement(nm): 2.562560 ± 0.133567
Precession(°): 51.19390 ± 6.14283

  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.