Trajectory SP924

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: 39851
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P251 AP00144
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

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Sequence :
IGKFLHSAKKFGKAFVGEIMNS
Total charge (e): +3
Number of residues: 22
By amino acid:
  Basic: 7
  Acidic: 1
  Hydrophobic: 13
  Polar: 3
Electrostatic Dipolar Moment (e nm): 7.49
Longitudinal (e nm): 7.14
Transversal (e nm): 2.25
Hydrophobic Dipolar Moment (nm): 2.12
Longitudinal (nm): 1.42
Transversal (nm): 1.58
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): 0.636530000 ± 0.000865421
Upper leaflet (nm2): 0.636530000 ± 0.000865421
Lower leaflet (nm2): 0.636530000 ± 0.000865421
Average Z coordinate
Peptide (nm): 8.0266700 ± 0.0341495
First Residue (nm): 7.8478700 ± 0.0456731
Last Residue (nm): 8.1233500 ± 0.0433556
Membrane (nm): 6.04433000 ± 0.00787063
Upper leaflet Head Group (nm): 8.03757000 ± 0.00965824
Lower leaflet Head Group (nm): 4.05189000 ± 0.00643659
Bilayer Thickness (nm): 3.9856800 ± 0.0116065
Peptide insertion (nm): -0.0108958 ± 0.0354890
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 13.880000 ± 0.317035
Peptide - Tail groups: 12.397500 ± 0.256716
Tilt (°): 87.59610 ± 0.92835
PepDF:
5(ns):  CVS
Displacement (nm): 0.5363040 ± 0.0219988
Precession(°): 0.369585 ± 1.093770
50(ns)  CVS
Displacement (nm): 1.866090 ± 0.100655
Precession(°): 4.36359 ± 3.33007
100(ns)  CVS
Displacement(nm): 2.571630 ± 0.141511
Precession(°): 8.52459 ± 3.59262
200(ns)  CVS
Displacement(nm): 4.360940 ± 0.157446
Precession(°): 19.1317 ± 4.4970

  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.