Trajectory SP1465

Force field: martini_v3
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: 17404
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P521 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): 1.17
Transversal (e nm): 1.13
Hydrophobic Dipolar Moment (nm): 7.29
Longitudinal (nm): 7.19
Transversal (nm): 1.2
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): 0.61394500 ± 0.00100297
Upper leaflet (nm2): 0.61394500 ± 0.00100297
Lower leaflet (nm2): 0.61394500 ± 0.00100297
Average Z coordinate
Peptide (nm): 9.0696400 ± 0.0530303
First Residue (nm): 8.5184100 ± 0.0538793
Last Residue (nm): 9.888850 ± 0.108626
Membrane (nm): 6.4071700 ± 0.0101519
Upper leaflet Head Group (nm): 8.421400 ± 0.012183
Lower leaflet Head Group (nm): 4.39253000 ± 0.00828234
Bilayer Thickness (nm): 4.0288700 ± 0.0147317
Peptide insertion (nm): 0.6482390 ± 0.0544118
Contacts
Peptide - Water: 63.08750 ± 1.46269
Peptide - Head groups: 8.430000 ± 0.472307
Peptide - Tail groups: 5.097500 ± 0.234615
Tilt (°): 58.5344 ± 2.8256
PepDF:
5(ns):  CVS
Displacement (nm): 0.8603910 ± 0.0359116
Precession(°): 2.61624 ± 3.42725
50(ns)  CVS
Displacement (nm): 2.373120 ± 0.110171
Precession(°): 21.21130 ± 9.42098
100(ns)  CVS
Displacement(nm): 3.139460 ± 0.159111
Precession(°): 35.0827 ± 12.5234
200(ns)  CVS
Displacement(nm): 4.42459 ± 0.18340
Precession(°): 47.2748 ± 21.0202

  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.