Trajectory SP1213

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: 17404
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P395 AP00492
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
QRVEELSKFSKKGAAARRRK
Total charge (e): +6
Number of residues: 20
By amino acid:
  Basic: 8
  Acidic: 2
  Hydrophobic: 7
  Polar: 3
Electrostatic Dipolar Moment (e nm): 0.57
Longitudinal (e nm): 0.19
Transversal (e nm): 0.54
Hydrophobic Dipolar Moment (nm): 4.74
Longitudinal (nm): 4.53
Transversal (nm): 1.37
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): 0.6141840 ± 0.0011057
Upper leaflet (nm2): 0.6141840 ± 0.0011057
Lower leaflet (nm2): 0.6141840 ± 0.0011057
Average Z coordinate
Peptide (nm): 3.659010 ± 0.271668
First Residue (nm): 3.874400 ± 0.287712
Last Residue (nm): 3.378880 ± 0.295079
Membrane (nm): 6.4028300 ± 0.0114344
Upper leaflet Head Group (nm): 8.4157900 ± 0.0135839
Lower leaflet Head Group (nm): 4.39083000 ± 0.00965035
Bilayer Thickness (nm): 4.0249700 ± 0.0166629
Peptide insertion (nm): 0.731814 ± 0.271840
Contacts
Peptide - Water: 70.6225 ± 6.8605
Peptide - Head groups: 7.7375 ± 2.3514
Peptide - Tail groups: 3.73250 ± 1.31307
Tilt (°): 78.0075 ± 5.2474
PepDF:
5(ns):  CVS
Displacement (nm): 0.9237370 ± 0.0492143
Precession(°): -0.327877 ± 3.859010
50(ns)  CVS
Displacement (nm): 2.770000 ± 0.174436
Precession(°): -1.22046 ± 11.96630
100(ns)  CVS
Displacement(nm): 3.438660 ± 0.262443
Precession(°): 11.6420 ± 13.3228
200(ns)  CVS
Displacement(nm): 4.557020 ± 0.270152
Precession(°): 31.6513 ± 20.2238

  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.