Trajectory SP1325

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: P451 AP03488
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
LWENFKNAGKKFILNILDKIRCRVAGGCRT
Total charge (e): +5
Number of residues: 30
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 15
  Polar: 6
Electrostatic Dipolar Moment (e nm): 2.27
Longitudinal (e nm): 2.24
Transversal (e nm): 0.37
Hydrophobic Dipolar Moment (nm): 4.11
Longitudinal (nm): 3.89
Transversal (nm): 1.32
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): 0.614484000 ± 0.000942362
Upper leaflet (nm2): 0.614484000 ± 0.000942362
Lower leaflet (nm2): 0.614484000 ± 0.000942362
Average Z coordinate
Peptide (nm): 8.6660200 ± 0.0426932
First Residue (nm): 8.4812500 ± 0.0601006
Last Residue (nm): 8.9724700 ± 0.0535316
Membrane (nm): 6.39399000 ± 0.00961893
Upper leaflet Head Group (nm): 8.4044100 ± 0.0110698
Lower leaflet Head Group (nm): 4.38295000 ± 0.00817101
Bilayer Thickness (nm): 4.0214600 ± 0.0137589
Peptide insertion (nm): 0.2616090 ± 0.0441049
Contacts
Peptide - Water: 61.22750 ± 0.93401
Peptide - Head groups: 15.612500 ± 0.349496
Peptide - Tail groups: 13.605000 ± 0.297643
Tilt (°): 85.63810 ± 1.00428
PepDF:
5(ns):  CVS
Displacement (nm): 0.6145540 ± 0.0240243
Precession(°): 1.07233 ± 1.32974
50(ns)  CVS
Displacement (nm): 1.5180900 ± 0.0728039
Precession(°): 7.83769 ± 4.36363
100(ns)  CVS
Displacement(nm): 1.9603100 ± 0.0780949
Precession(°): 15.24660 ± 5.93635
200(ns)  CVS
Displacement(nm): 2.475660 ± 0.107944
Precession(°): 34.87790 ± 7.17645

  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.