Trajectory SP1114

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: 39874
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P346 NC00701
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
LPHPVLHMGPLR
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 7
  Acidic: 0
  Hydrophobic: 9
  Polar: 0
Electrostatic Dipolar Moment (e nm): 1.32
Longitudinal (e nm): 1.14
Transversal (e nm): 0.67
Hydrophobic Dipolar Moment (nm): 1.72
Longitudinal (nm): 1.71
Transversal (nm): 0.14
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): 0.635535000 ± 0.000948075
Upper leaflet (nm2): 0.635535000 ± 0.000948075
Lower leaflet (nm2): 0.635535000 ± 0.000948075
Average Z coordinate
Peptide (nm): 7.8900500 ± 0.0381387
First Residue (nm): 7.8087300 ± 0.0397868
Last Residue (nm): 8.1390100 ± 0.0529201
Membrane (nm): 6.05619000 ± 0.00870276
Upper leaflet Head Group (nm): 8.0516900 ± 0.0104364
Lower leaflet Head Group (nm): 4.06126000 ± 0.00695839
Bilayer Thickness (nm): 3.9904200 ± 0.0125435
Peptide insertion (nm): -0.1616330 ± 0.0395409
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 10.06000 ± 0.30562
Peptide - Tail groups: 8.600000 ± 0.311323
Tilt (°): 81.00460 ± 1.69456
PepDF:
5(ns):  CVS
Displacement (nm): 0.6274640 ± 0.0255517
Precession(°): 0.992524 ± 1.936410
50(ns)  CVS
Displacement (nm): 1.7658300 ± 0.0765721
Precession(°): 10.2853 ± 7.8989
100(ns)  CVS
Displacement(nm): 2.445500 ± 0.117189
Precession(°): 23.3219 ± 13.0488
200(ns)  CVS
Displacement(nm): 3.634280 ± 0.155177
Precession(°): 48.6751 ± 19.7782

  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.