Trajectory SP1279

Force field: martini_v3
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: 17407
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P428 AP02645
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
EDLPNFGHIQVKVFNHGEHIHH
Total charge (e): -2
Number of residues: 22
By amino acid:
  Basic: 16
  Acidic: 3
  Hydrophobic: 10
  Polar: 3
Electrostatic Dipolar Moment (e nm): 0.95
Longitudinal (e nm): 0.81
Transversal (e nm): 0.49
Hydrophobic Dipolar Moment (nm): 1.36
Longitudinal (nm): 0.35
Transversal (nm): 1.31
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): 0.61387600 ± 0.00109846
Upper leaflet (nm2): 0.61387600 ± 0.00109846
Lower leaflet (nm2): 0.61387600 ± 0.00109846
Average Z coordinate
Peptide (nm): 3.8553400 ± 0.0569386
First Residue (nm): 3.599430 ± 0.149008
Last Residue (nm): 3.837840 ± 0.165824
Membrane (nm): 6.4016200 ± 0.0110771
Upper leaflet Head Group (nm): 8.4140700 ± 0.0131344
Lower leaflet Head Group (nm): 4.39176000 ± 0.00914065
Bilayer Thickness (nm): 4.022310 ± 0.016002
Peptide insertion (nm): 0.5364140 ± 0.0576677
Contacts
Peptide - Water: 58.49750 ± 2.31871
Peptide - Head groups: 10.820000 ± 0.592945
Peptide - Tail groups: 7.85750 ± 0.59382
Tilt (°): 95.04820 ± 7.13011
PepDF:
5(ns):  CVS
Displacement (nm): 0.7522410 ± 0.0334957
Precession(°): 0.0276304 ± 2.3421500
50(ns)  CVS
Displacement (nm): 2.183180 ± 0.118856
Precession(°): 5.18604 ± 9.93360
100(ns)  CVS
Displacement(nm): 3.184980 ± 0.151119
Precession(°): 11.3829 ± 14.9583
200(ns)  CVS
Displacement(nm): 4.579300 ± 0.251069
Precession(°): -3.14971 ± 17.84860

  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.