Trajectory SP1008

Force field: martini_v2.2P
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: 39866
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P293 AP02666
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

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Sequence :
VAGEKLWLLPHLLKMLLTPTP
Total charge (e): +1
Number of residues: 21
By amino acid:
  Basic: 5
  Acidic: 1
  Hydrophobic: 15
  Polar: 2
Electrostatic Dipolar Moment (e nm): 3.14
Longitudinal (e nm): 3.12
Transversal (e nm): 0.32
Hydrophobic Dipolar Moment (nm): 2.01
Longitudinal (nm): 1.89
Transversal (nm): 0.69
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): 0.637158000 ± 0.000940464
Upper leaflet (nm2): 0.637158000 ± 0.000940464
Lower leaflet (nm2): 0.637158000 ± 0.000940464
Average Z coordinate
Peptide (nm): 7.8408700 ± 0.0367295
First Residue (nm): 7.8549200 ± 0.0534091
Last Residue (nm): 7.8027400 ± 0.0428233
Membrane (nm): 6.04023000 ± 0.00940035
Upper leaflet Head Group (nm): 8.0341700 ± 0.0114472
Lower leaflet Head Group (nm): 4.04843000 ± 0.00725503
Bilayer Thickness (nm): 3.9857400 ± 0.0135526
Peptide insertion (nm): -0.193297 ± 0.038472
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 12.722500 ± 0.326021
Peptide - Tail groups: 12.795000 ± 0.300326
Tilt (°): 88.83390 ± 1.21276
PepDF:
5(ns):  CVS
Displacement (nm): 0.5352950 ± 0.0206795
Precession(°): 0.592451 ± 1.181950
50(ns)  CVS
Displacement (nm): 1.4666600 ± 0.0680543
Precession(°): 4.84242 ± 3.64019
100(ns)  CVS
Displacement(nm): 1.97378 ± 0.10581
Precession(°): 8.74412 ± 4.62611
200(ns)  CVS
Displacement(nm): 2.564920 ± 0.128374
Precession(°): 8.97932 ± 4.74185

  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.