Trajectory SP1439

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: P508 NC02924
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
VKLPPPVKLPPPVKLPPP
Total charge (e): +3
Number of residues: 18
By amino acid:
  Basic: 3
  Acidic: 0
  Hydrophobic: 15
  Polar: 0
Electrostatic Dipolar Moment (e nm): 4.41
Longitudinal (e nm): 4.41
Transversal (e nm): 0.18
Hydrophobic Dipolar Moment (nm): 0.42
Longitudinal (nm): 0.4
Transversal (nm): 0.13
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): 0.6149110 ± 0.0011294
Upper leaflet (nm2): 0.6149110 ± 0.0011294
Lower leaflet (nm2): 0.6149110 ± 0.0011294
Average Z coordinate
Peptide (nm): 4.2738600 ± 0.0322855
First Residue (nm): 4.265830 ± 0.040082
Last Residue (nm): 4.2069400 ± 0.0504034
Membrane (nm): 6.3974800 ± 0.0117897
Upper leaflet Head Group (nm): 8.4078300 ± 0.0140951
Lower leaflet Head Group (nm): 4.38631000 ± 0.00951621
Bilayer Thickness (nm): 4.0215300 ± 0.0170068
Peptide insertion (nm): 0.1124530 ± 0.0336587
Contacts
Peptide - Water: 32.410000 ± 0.875519
Peptide - Head groups: 10.32250 ± 0.30332
Peptide - Tail groups: 10.21750 ± 0.30283
Tilt (°): 93.41150 ± 1.44704
PepDF:
5(ns):  CVS
Displacement (nm): 0.7369160 ± 0.0297056
Precession(°): 4.2488 ± 2.2692
50(ns)  CVS
Displacement (nm): 2.085480 ± 0.104316
Precession(°): 41.55650 ± 8.02353
100(ns)  CVS
Displacement(nm): 2.987730 ± 0.143287
Precession(°): 77.53570 ± 9.28578
200(ns)  CVS
Displacement(nm): 4.026520 ± 0.283911
Precession(°): 153.8820 ± 13.4668

  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.