Trajectory SP675

Force field: martini_v2.2
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: 17381
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P127 AP00955
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
IIRPIIQIIKQKIR
Total charge (e): +4
Number of residues: 14
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.11
Longitudinal (e nm): 1.87
Transversal (e nm): 0.98
Hydrophobic Dipolar Moment (nm): 4.53
Longitudinal (nm): 4.43
Transversal (nm): 0.94
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)
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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): 0.60634300 ± 0.00116334
Upper leaflet (nm2): 0.60634300 ± 0.00116334
Lower leaflet (nm2): 0.60634300 ± 0.00116334
Average Z coordinate
Peptide (nm): 8.446420 ± 0.039998
First Residue (nm): 8.2894200 ± 0.0525318
Last Residue (nm): 8.581780 ± 0.044693
Membrane (nm): 6.5201400 ± 0.0123768
Upper leaflet Head Group (nm): 8.548650 ± 0.014841
Lower leaflet Head Group (nm): 4.4933900 ± 0.0101874
Bilayer Thickness (nm): 4.0552700 ± 0.0180011
Peptide insertion (nm): -0.1022350 ± 0.0426626
Contacts
Peptide - Water: 22.865000 ± 0.553114
Peptide - Head groups: 10.832500 ± 0.269282
Peptide - Tail groups: 9.505000 ± 0.240294
Tilt (°): 86.87320 ± 1.50813
PepDF:
5(ns):  CVS
Displacement (nm): 0.6745200 ± 0.0279873
Precession(°): -1.49304 ± 2.12440
50(ns)  CVS
Displacement (nm): 1.9323000 ± 0.0906015
Precession(°): -17.25640 ± 6.86811
100(ns)  CVS
Displacement(nm): 2.57256 ± 0.11112
Precession(°): -38.0147 ± 10.1371
200(ns)  CVS
Displacement(nm): 3.438530 ± 0.145314
Precession(°): -79.0515 ± 14.6149

  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.