Trajectory SP976

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: P277 AP01545
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
FGHLFKLATKIIPSLFQ
Total charge (e): +2
Number of residues: 17
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 11
  Polar: 3
Electrostatic Dipolar Moment (e nm): 3.49
Longitudinal (e nm): 3.29
Transversal (e nm): 1.15
Hydrophobic Dipolar Moment (nm): 1.48
Longitudinal (nm): 0.1
Transversal (nm): 1.47
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): 0.63684900 ± 0.00107913
Upper leaflet (nm2): 0.63684900 ± 0.00107913
Lower leaflet (nm2): 0.63684900 ± 0.00107913
Average Z coordinate
Peptide (nm): 7.8873900 ± 0.0414051
First Residue (nm): 7.8725400 ± 0.0462726
Last Residue (nm): 8.1098600 ± 0.0468554
Membrane (nm): 6.0423400 ± 0.0105388
Upper leaflet Head Group (nm): 8.0366900 ± 0.0125694
Lower leaflet Head Group (nm): 4.05016000 ± 0.00812706
Bilayer Thickness (nm): 3.9865300 ± 0.0149679
Peptide insertion (nm): -0.1493070 ± 0.0432709
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 12.635000 ± 0.236623
Peptide - Tail groups: 11.895000 ± 0.268253
Tilt (°): 89.02600 ± 0.94567
PepDF:
5(ns):  CVS
Displacement (nm): 0.6032470 ± 0.0240624
Precession(°): -1.25977 ± 1.22848
50(ns)  CVS
Displacement (nm): 2.0110200 ± 0.0958509
Precession(°): -11.47430 ± 3.88501
100(ns)  CVS
Displacement(nm): 2.623740 ± 0.160238
Precession(°): -24.36850 ± 5.61707
200(ns)  CVS
Displacement(nm): 3.884300 ± 0.244253
Precession(°): -54.80450 ± 6.48907

  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.