Trajectory SP1233

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: 17403
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P405 AP01015
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
LKDKVKSMGEKLKQYIQTWKAKF
Total charge (e): +5
Number of residues: 23
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 9
  Polar: 5
Electrostatic Dipolar Moment (e nm): 5.23
Longitudinal (e nm): 5.19
Transversal (e nm): 0.7
Hydrophobic Dipolar Moment (nm): 5.29
Longitudinal (nm): 4.92
Transversal (nm): 1.97
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): 0.614605000 ± 0.000958813
Upper leaflet (nm2): 0.614605000 ± 0.000958813
Lower leaflet (nm2): 0.614605000 ± 0.000958813
Average Z coordinate
Peptide (nm): 8.6634500 ± 0.0425816
First Residue (nm): 8.5264900 ± 0.0418399
Last Residue (nm): 8.6139300 ± 0.0577531
Membrane (nm): 6.39686000 ± 0.00948219
Upper leaflet Head Group (nm): 8.4078400 ± 0.0112762
Lower leaflet Head Group (nm): 4.38525000 ± 0.00790378
Bilayer Thickness (nm): 4.0225900 ± 0.0137704
Peptide insertion (nm): 0.2556160 ± 0.0440494
Contacts
Peptide - Water: 51.80250 ± 0.98864
Peptide - Head groups: 13.91000 ± 0.39686
Peptide - Tail groups: 11.515000 ± 0.300642
Tilt (°): 88.798000 ± 0.999898
PepDF:
5(ns):  CVS
Displacement (nm): 0.6647270 ± 0.0276325
Precession(°): -0.439222 ± 1.568170
50(ns)  CVS
Displacement (nm): 1.7387900 ± 0.0892458
Precession(°): -5.60076 ± 4.98931
100(ns)  CVS
Displacement(nm): 2.147800 ± 0.104177
Precession(°): -9.87549 ± 7.44418
200(ns)  CVS
Displacement(nm): 2.68976 ± 0.13603
Precession(°): -10.2844 ± 12.2180

  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.