Trajectory SP282

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: 24844
Time step (fs) : 25
Software: GROMACS 2020
Supercomputer: Finisterrae II CESGA
Peptides: P47 NC00004
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

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Sequence :
GCCSNPVCFATHSNLC
Total charge (e): 0
Number of residues: 16
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 6
  Polar: 9
Electrostatic Dipolar Moment (e nm): 2.46
Longitudinal (e nm): 2.46
Transversal (e nm): 0
Hydrophobic Dipolar Moment (nm): 0.8
Longitudinal (nm): 0.47
Transversal (nm): 0.65
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
 
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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): 0.60386 ± 0.00056
Upper leaflet (nm2): 0.60386 ± 0.00056
Lower leaflet (nm2): 0.60386 ± 0.00056
Average Z coordinate
Peptide (nm): 11.614 ± 0.030
First Residue (nm): 11.539 ± 0.029
Last Residue (nm): 11.871 ± 0.048
Membrane (nm): 9.4777 ± 0.0086
Upper leaflet Head Group (nm): 11.5076 ± 0.0098
Lower leaflet Head Group (nm): 7.4478 ± 0.0076
Bilayer Thickness (nm): 4.060 ± 0.012
Peptide insertion (nm): 0.106 ± 0.032
Contacts
Peptide - Water: 24.43 ± 0.48
Peptide - Head groups: 10.52 ± 0.17
Peptide - Tail groups: 8.49 ± 0.19
Tilt (°): 80.6 ± 1.3
PepDF:
5(ns):  CVS
Displacement (nm): 0.805 ± 0.048
Precession(°): -1.4 ± 4.1
50(ns)  CVS
Displacement (nm): 2.78 ± 0.41
Precession(°): -14.0 ± 35.0
100(ns)  CVS
Displacement(nm): 4.2 ± 1.1
Precession(°): -25.0 ± 71.0
200(ns)  CVS
Displacement(nm): 5.6 ± 1.3
Precession(°): -20.0 ± 120.0

  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.