Trajectory SP962

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: 39828
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P270 AP01018
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
AFQTFKPDWNKIRYDAMKMQTSLGQMKKRFNL
Total charge (e): +5
Number of residues: 32
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 14
  Polar: 9
Electrostatic Dipolar Moment (e nm): 2.68
Longitudinal (e nm): 2.26
Transversal (e nm): 1.44
Hydrophobic Dipolar Moment (nm): 4.45
Longitudinal (nm): 4.15
Transversal (nm): 1.59
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): 0.63681400 ± 0.00100424
Upper leaflet (nm2): 0.63681400 ± 0.00100424
Lower leaflet (nm2): 0.63681400 ± 0.00100424
Average Z coordinate
Peptide (nm): 8.1612300 ± 0.0342228
First Residue (nm): 8.0118500 ± 0.0451501
Last Residue (nm): 8.5572400 ± 0.0571051
Membrane (nm): 6.04038000 ± 0.00916057
Upper leaflet Head Group (nm): 8.0307900 ± 0.0109748
Lower leaflet Head Group (nm): 4.0494400 ± 0.0073994
Bilayer Thickness (nm): 3.9813500 ± 0.0132362
Peptide insertion (nm): 0.1304390 ± 0.0359395
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 18.417500 ± 0.348206
Peptide - Tail groups: 15.015000 ± 0.319716
Tilt (°): 86.900000 ± 0.969491
PepDF:
5(ns):  CVS
Displacement (nm): 0.5151850 ± 0.0216328
Precession(°): 0.588248 ± 0.756396
50(ns)  CVS
Displacement (nm): 1.455300 ± 0.068146
Precession(°): 8.66901 ± 2.31011
100(ns)  CVS
Displacement(nm): 1.924610 ± 0.112833
Precession(°): 17.24440 ± 3.26906
200(ns)  CVS
Displacement(nm): 2.518430 ± 0.159194
Precession(°): 26.95100 ± 4.00144

  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.