Trajectory SP1072

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: 39863
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P325 AP03758
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
GLRSLGRKILRAWKKYGPQATPATRQ
Total charge (e): +7
Number of residues: 26
By amino acid:
  Basic: 7
  Acidic: 0
  Hydrophobic: 13
  Polar: 6
Electrostatic Dipolar Moment (e nm): 8.72
Longitudinal (e nm): 8.35
Transversal (e nm): 2.5
Hydrophobic Dipolar Moment (nm): 3.8
Longitudinal (nm): 3.27
Transversal (nm): 1.94
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): 0.636833000 ± 0.000950423
Upper leaflet (nm2): 0.636833000 ± 0.000950423
Lower leaflet (nm2): 0.636833000 ± 0.000950423
Average Z coordinate
Peptide (nm): 7.9537500 ± 0.0303299
First Residue (nm): 7.811800 ± 0.043594
Last Residue (nm): 8.3881700 ± 0.0410501
Membrane (nm): 6.04160000 ± 0.00854127
Upper leaflet Head Group (nm): 8.0353500 ± 0.0103342
Lower leaflet Head Group (nm): 4.04964000 ± 0.00672757
Bilayer Thickness (nm): 3.9857100 ± 0.0123311
Peptide insertion (nm): -0.0816008 ± 0.0320421
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 16.845000 ± 0.343706
Peptide - Tail groups: 13.877500 ± 0.330798
Tilt (°): 83.96490 ± 0.89456
PepDF:
5(ns):  CVS
Displacement (nm): 0.5299320 ± 0.0225192
Precession(°): 0.994457 ± 0.931578
50(ns)  CVS
Displacement (nm): 1.5213100 ± 0.0751492
Precession(°): 8.84564 ± 2.93280
100(ns)  CVS
Displacement(nm): 2.184850 ± 0.111215
Precession(°): 15.37560 ± 4.47695
200(ns)  CVS
Displacement(nm): 3.476600 ± 0.174257
Precession(°): 23.04830 ± 6.35909

  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.