Trajectory SP1022

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: 39795
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P300 AP03031
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
LFSKKGGKGGKSWIKGVFKGIKGIGKEVGGDVIRT-
GIEIAACKIKGEC
Total charge (e): +7
Number of residues: 48
By amino acid:
  Basic: 11
  Acidic: 4
  Hydrophobic: 28
  Polar: 5
Electrostatic Dipolar Moment (e nm): 22.38
Longitudinal (e nm): 22.1
Transversal (e nm): 3.56
Hydrophobic Dipolar Moment (nm): 7.11
Longitudinal (nm): 7.02
Transversal (nm): 1.14
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): 0.640074000 ± 0.000994223
Upper leaflet (nm2): 0.640074000 ± 0.000994223
Lower leaflet (nm2): 0.640074000 ± 0.000994223
Average Z coordinate
Peptide (nm): 7.8431500 ± 0.0330002
First Residue (nm): 7.7881000 ± 0.0533757
Last Residue (nm): 8.2850600 ± 0.0481292
Membrane (nm): 6.00559000 ± 0.00920008
Upper leaflet Head Group (nm): 7.9943300 ± 0.0109301
Lower leaflet Head Group (nm): 4.02050000 ± 0.00745382
Bilayer Thickness (nm): 3.9738200 ± 0.0132298
Peptide insertion (nm): -0.1511720 ± 0.0347632
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 24.635000 ± 0.446785
Peptide - Tail groups: 24.852500 ± 0.414267
Tilt (°): 88.355900 ± 0.547484
PepDF:
5(ns):  CVS
Displacement (nm): 0.5704610 ± 0.0233456
Precession(°): -0.019986 ± 0.121212
50(ns)  CVS
Displacement (nm): 1.4237200 ± 0.0698276
Precession(°): -0.112897 ± 0.259926
100(ns)  CVS
Displacement(nm): 2.086330 ± 0.114543
Precession(°): -0.151861 ± 0.228757
200(ns)  CVS
Displacement(nm): 2.884300 ± 0.168217
Precession(°): -0.122185 ± 0.257795

  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.