Trajectory SP1455

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: 17401
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P516 NC03705
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
HIQLSPFSQSWR
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 5
  Polar: 5
Electrostatic Dipolar Moment (e nm): 1.45
Longitudinal (e nm): 1.27
Transversal (e nm): 0.7
Hydrophobic Dipolar Moment (nm): 1.46
Longitudinal (nm): 1.33
Transversal (nm): 0.59
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)
  Download PDB File.

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): 0.61417300 ± 0.00097075
Upper leaflet (nm2): 0.61417300 ± 0.00097075
Lower leaflet (nm2): 0.61417300 ± 0.00097075
Average Z coordinate
Peptide (nm): 8.5919100 ± 0.0337939
First Residue (nm): 8.6572100 ± 0.0437068
Last Residue (nm): 8.8851200 ± 0.0433792
Membrane (nm): 6.40341000 ± 0.00952199
Upper leaflet Head Group (nm): 8.417030 ± 0.011822
Lower leaflet Head Group (nm): 4.38930000 ± 0.00748994
Bilayer Thickness (nm): 4.027730 ± 0.013995
Peptide insertion (nm): 0.174886 ± 0.035802
Contacts
Peptide - Water: 30.817500 ± 0.722457
Peptide - Head groups: 8.387500 ± 0.287418
Peptide - Tail groups: 7.187500 ± 0.345027
Tilt (°): 83.12090 ± 1.91433
PepDF:
5(ns):  CVS
Displacement (nm): 0.8560220 ± 0.0350379
Precession(°): 0.814349 ± 4.027920
50(ns)  CVS
Displacement (nm): 2.420310 ± 0.108251
Precession(°): 5.57218 ± 14.38980
100(ns)  CVS
Displacement(nm): 3.334900 ± 0.166061
Precession(°): 29.8205 ± 17.9254
200(ns)  CVS
Displacement(nm): 4.220720 ± 0.203648
Precession(°): 97.6278 ± 23.4637

  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.