Trajectory SP1080

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: 39869
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P329 AP03826
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
KWVKKVVKWVKKV
Total charge (e): +6
Number of residues: 13
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 7
  Polar: 0
Electrostatic Dipolar Moment (e nm): 4.05
Longitudinal (e nm): 3.56
Transversal (e nm): 1.92
Hydrophobic Dipolar Moment (nm): 1.8
Longitudinal (nm): 0.11
Transversal (nm): 1.79
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): 0.635800000 ± 0.000888257
Upper leaflet (nm2): 0.635800000 ± 0.000888257
Lower leaflet (nm2): 0.635800000 ± 0.000888257
Average Z coordinate
Peptide (nm): 7.8919700 ± 0.0388513
First Residue (nm): 7.909770 ± 0.042811
Last Residue (nm): 7.8334000 ± 0.0436198
Membrane (nm): 6.05195000 ± 0.00825849
Upper leaflet Head Group (nm): 8.0479000 ± 0.0100973
Lower leaflet Head Group (nm): 4.0580100 ± 0.0066638
Bilayer Thickness (nm): 3.989890 ± 0.012098
Peptide insertion (nm): -0.155929 ± 0.040142
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 11.165000 ± 0.232201
Peptide - Tail groups: 9.455000 ± 0.288124
Tilt (°): 86.0745 ± 1.4164
PepDF:
5(ns):  CVS
Displacement (nm): 0.562752 ± 0.022234
Precession(°): 0.664978 ± 1.376250
50(ns)  CVS
Displacement (nm): 1.4663700 ± 0.0792457
Precession(°): 6.21826 ± 4.40503
100(ns)  CVS
Displacement(nm): 2.136670 ± 0.132169
Precession(°): 10.78380 ± 6.57854
200(ns)  CVS
Displacement(nm): 3.10733 ± 0.22131
Precession(°): 15.11590 ± 8.92691

  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.