Trajectory SP992

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: 39858
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P285 AP02162
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

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Sequence :
IKIPWGKVKDFLVGGMKAV
Total charge (e): +3
Number of residues: 19
By amino acid:
  Basic: 4
  Acidic: 1
  Hydrophobic: 14
  Polar: 0
Electrostatic Dipolar Moment (e nm): 4.37
Longitudinal (e nm): 4.29
Transversal (e nm): 0.84
Hydrophobic Dipolar Moment (nm): 2.35
Longitudinal (nm): 2.02
Transversal (nm): 1.19
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
 
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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): 0.636371000 ± 0.000969158
Upper leaflet (nm2): 0.636371000 ± 0.000969158
Lower leaflet (nm2): 0.636371000 ± 0.000969158
Average Z coordinate
Peptide (nm): 7.9053000 ± 0.0439446
First Residue (nm): 7.8137600 ± 0.0475199
Last Residue (nm): 7.8371300 ± 0.0567854
Membrane (nm): 6.04676000 ± 0.00897185
Upper leaflet Head Group (nm): 8.0419500 ± 0.0105804
Lower leaflet Head Group (nm): 4.05384000 ± 0.00736429
Bilayer Thickness (nm): 3.988120 ± 0.012891
Peptide insertion (nm): -0.1366580 ± 0.0452003
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 12.092500 ± 0.271668
Peptide - Tail groups: 12.160000 ± 0.246326
Tilt (°): 87.64080 ± 1.25928
PepDF:
5(ns):  CVS
Displacement (nm): 0.5512580 ± 0.0228261
Precession(°): -0.942629 ± 1.221640
50(ns)  CVS
Displacement (nm): 1.6077900 ± 0.0893316
Precession(°): -11.36060 ± 3.83673
100(ns)  CVS
Displacement(nm): 1.9681900 ± 0.0999658
Precession(°): -21.63850 ± 4.18361
200(ns)  CVS
Displacement(nm): 2.564810 ± 0.116908
Precession(°): -50.3478 ± 4.8236

  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.