Trajectory SP936

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: 39841
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P257 AP00476
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
LNALKKVFQGIHEAIKLINNHVQ
Total charge (e): +2
Number of residues: 23
By amino acid:
  Basic: 9
  Acidic: 1
  Hydrophobic: 12
  Polar: 5
Electrostatic Dipolar Moment (e nm): 5.98
Longitudinal (e nm): 5.87
Transversal (e nm): 1.15
Hydrophobic Dipolar Moment (nm): 2.72
Longitudinal (nm): 1.43
Transversal (nm): 2.31
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): 0.63692000 ± 0.00111464
Upper leaflet (nm2): 0.63692000 ± 0.00111464
Lower leaflet (nm2): 0.63692000 ± 0.00111464
Average Z coordinate
Peptide (nm): 7.9013500 ± 0.0364168
First Residue (nm): 7.7765900 ± 0.0402458
Last Residue (nm): 8.1076900 ± 0.0420309
Membrane (nm): 6.03878000 ± 0.00997874
Upper leaflet Head Group (nm): 8.0332000 ± 0.0120184
Lower leaflet Head Group (nm): 4.0470700 ± 0.0078902
Bilayer Thickness (nm): 3.986130 ± 0.014377
Peptide insertion (nm): -0.1318450 ± 0.0383488
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 15.067500 ± 0.346096
Peptide - Tail groups: 13.380000 ± 0.301496
Tilt (°): 84.196100 ± 0.850831
PepDF:
5(ns):  CVS
Displacement (nm): 0.5409010 ± 0.0222398
Precession(°): 0.976640 ± 0.945635
50(ns)  CVS
Displacement (nm): 1.5388500 ± 0.0784748
Precession(°): 11.69990 ± 3.19784
100(ns)  CVS
Displacement(nm): 2.28289 ± 0.13553
Precession(°): 23.9732 ± 4.5283
200(ns)  CVS
Displacement(nm): 3.32724 ± 0.18964
Precession(°): 47.59590 ± 6.88157

  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.