Trajectory SP915

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: 17378
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P247 NC04227
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
SPWSQCSVRCGRGQRSRQVR
Total charge (e): +5
Number of residues: 20
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 6
  Polar: 9
Electrostatic Dipolar Moment (e nm): 1.62
Longitudinal (e nm): 1.23
Transversal (e nm): 1.06
Hydrophobic Dipolar Moment (nm): 7.22
Longitudinal (nm): 7.12
Transversal (nm): 1.19
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): 0.605662000 ± 0.000880901
Upper leaflet (nm2): 0.605662000 ± 0.000880901
Lower leaflet (nm2): 0.605662000 ± 0.000880901
Average Z coordinate
Peptide (nm): 8.8129400 ± 0.0431789
First Residue (nm): 8.5412600 ± 0.0463436
Last Residue (nm): 9.2590400 ± 0.0784781
Membrane (nm): 6.52351000 ± 0.00910686
Upper leaflet Head Group (nm): 8.5511600 ± 0.0109873
Lower leaflet Head Group (nm): 4.49560000 ± 0.00738998
Bilayer Thickness (nm): 4.0555600 ± 0.0132414
Peptide insertion (nm): 0.2617880 ± 0.0445549
Contacts
Peptide - Water: 41.04750 ± 1.63895
Peptide - Head groups: 13.340000 ± 0.445193
Peptide - Tail groups: 8.270000 ± 0.402796
Tilt (°): 74.13590 ± 1.90638
PepDF:
5(ns):  CVS
Displacement (nm): 0.673917 ± 0.026535
Precession(°): -1.13169 ± 1.88123
50(ns)  CVS
Displacement (nm): 2.013880 ± 0.103278
Precession(°): -12.99350 ± 5.91226
100(ns)  CVS
Displacement(nm): 3.062660 ± 0.183234
Precession(°): -22.70210 ± 8.88464
200(ns)  CVS
Displacement(nm): 4.485780 ± 0.311269
Precession(°): -29.6550 ± 13.7757

  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.