Trajectory SP701

Force field: martini_v2.2
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: 17383
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P140 AP01545
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  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): 3.38
Longitudinal (e nm): 3.14
Transversal (e nm): 1.25
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)
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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): 0.606309000 ± 0.000899899
Upper leaflet (nm2): 0.606309000 ± 0.000899899
Lower leaflet (nm2): 0.606309000 ± 0.000899899
Average Z coordinate
Peptide (nm): 8.4111100 ± 0.0354118
First Residue (nm): 8.3888500 ± 0.0479712
Last Residue (nm): 8.6918800 ± 0.0506641
Membrane (nm): 6.51789000 ± 0.00970599
Upper leaflet Head Group (nm): 8.5464200 ± 0.0116236
Lower leaflet Head Group (nm): 4.49084000 ± 0.00777938
Bilayer Thickness (nm): 4.0555800 ± 0.0139867
Peptide insertion (nm): -0.1353090 ± 0.0372707
Contacts
Peptide - Water: 23.24250 ± 0.64405
Peptide - Head groups: 12.360000 ± 0.263043
Peptide - Tail groups: 11.742500 ± 0.225999
Tilt (°): 87.57850 ± 1.52124
PepDF:
5(ns):  CVS
Displacement (nm): 0.644627 ± 0.025118
Precession(°): 0.842279 ± 1.681430
50(ns)  CVS
Displacement (nm): 1.8190700 ± 0.0960624
Precession(°): 10.56190 ± 4.99593
100(ns)  CVS
Displacement(nm): 2.379220 ± 0.140442
Precession(°): 23.15520 ± 6.09586
200(ns)  CVS
Displacement(nm): 3.478350 ± 0.157082
Precession(°): 53.26370 ± 5.82049

  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.