Trajectory SP685

Force field: martini_v2.2
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: 17382
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P132 AP01016
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
FFGKMKEYFKKFGASFKRRFANLKKRL
Total charge (e): +9
Number of residues: 27
By amino acid:
  Basic: 10
  Acidic: 1
  Hydrophobic: 13
  Polar: 3
Electrostatic Dipolar Moment (e nm): 2.23
Longitudinal (e nm): 1.53
Transversal (e nm): 1.62
Hydrophobic Dipolar Moment (nm): 7.15
Longitudinal (nm): 6.7
Transversal (nm): 2.51
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)
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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): 0.606196000 ± 0.000995607
Upper leaflet (nm2): 0.606196000 ± 0.000995607
Lower leaflet (nm2): 0.606196000 ± 0.000995607
Average Z coordinate
Peptide (nm): 8.5749500 ± 0.0371239
First Residue (nm): 8.5045900 ± 0.0584877
Last Residue (nm): 8.5407100 ± 0.0375907
Membrane (nm): 6.5120700 ± 0.0105471
Upper leaflet Head Group (nm): 8.539820 ± 0.012831
Lower leaflet Head Group (nm): 4.48650000 ± 0.00856858
Bilayer Thickness (nm): 4.0533200 ± 0.0154291
Peptide insertion (nm): 0.0351300 ± 0.0392788
Contacts
Peptide - Water: 43.975000 ± 0.819639
Peptide - Head groups: 18.067500 ± 0.332297
Peptide - Tail groups: 15.472500 ± 0.303281
Tilt (°): 89.314100 ± 0.915275
PepDF:
5(ns):  CVS
Displacement (nm): 0.554656 ± 0.021792
Precession(°): 0.131444 ± 1.069490
50(ns)  CVS
Displacement (nm): 1.3788800 ± 0.0664905
Precession(°): 2.34468 ± 2.80108
100(ns)  CVS
Displacement(nm): 1.8972400 ± 0.0957865
Precession(°): 5.41073 ± 2.87359
200(ns)  CVS
Displacement(nm): 2.642450 ± 0.137236
Precession(°): 9.33329 ± 3.62798

  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.