Trajectory SP1004

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: 39831
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P291 AP02645
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

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Sequence :
EDLPNFGHIQVKVFNHGEHIHH
Total charge (e): -2
Number of residues: 22
By amino acid:
  Basic: 16
  Acidic: 3
  Hydrophobic: 10
  Polar: 3
Electrostatic Dipolar Moment (e nm): 1.07
Longitudinal (e nm): 0.92
Transversal (e nm): 0.55
Hydrophobic Dipolar Moment (nm): 1.37
Longitudinal (nm): 0.37
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
 
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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): 0.636485000 ± 0.000918649
Upper leaflet (nm2): 0.636485000 ± 0.000918649
Lower leaflet (nm2): 0.636485000 ± 0.000918649
Average Z coordinate
Peptide (nm): 3.9051600 ± 0.0405768
First Residue (nm): 3.6627900 ± 0.0760597
Last Residue (nm): 3.8849100 ± 0.0410359
Membrane (nm): 6.04481000 ± 0.00867765
Upper leaflet Head Group (nm): 8.0371900 ± 0.0104421
Lower leaflet Head Group (nm): 4.05318000 ± 0.00691689
Bilayer Thickness (nm): 3.9840000 ± 0.0125252
Peptide insertion (nm): 0.1480240 ± 0.0411622
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 14.510000 ± 0.346805
Peptide - Tail groups: 11.485000 ± 0.408363
Tilt (°): 96.87310 ± 2.02207
PepDF:
5(ns):  CVS
Displacement (nm): 0.5426770 ± 0.0224543
Precession(°): -0.960892 ± 1.151650
50(ns)  CVS
Displacement (nm): 1.4551500 ± 0.0696903
Precession(°): -9.73728 ± 3.44228
100(ns)  CVS
Displacement(nm): 2.002780 ± 0.103269
Precession(°): -17.43390 ± 4.54794
200(ns)  CVS
Displacement(nm): 3.159270 ± 0.161486
Precession(°): -33.91220 ± 6.36121

  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.