Trajectory SP1160

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: 39876
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P369 NC02545
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
GRILSFIKAGLAEHL
Total charge (e): +1
Number of residues: 15
By amino acid:
  Basic: 5
  Acidic: 1
  Hydrophobic: 10
  Polar: 1
Electrostatic Dipolar Moment (e nm): 4.54
Longitudinal (e nm): 4.43
Transversal (e nm): 1
Hydrophobic Dipolar Moment (nm): 0.98
Longitudinal (nm): 0.13
Transversal (nm): 0.97
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): 0.63607200 ± 0.00105866
Upper leaflet (nm2): 0.63607200 ± 0.00105866
Lower leaflet (nm2): 0.63607200 ± 0.00105866
Average Z coordinate
Peptide (nm): 7.8693500 ± 0.0348455
First Residue (nm): 7.8923400 ± 0.0384877
Last Residue (nm): 7.8852300 ± 0.0439798
Membrane (nm): 6.05174000 ± 0.00950584
Upper leaflet Head Group (nm): 8.0466700 ± 0.0115963
Lower leaflet Head Group (nm): 4.05751000 ± 0.00758047
Bilayer Thickness (nm): 3.9891600 ± 0.0138541
Peptide insertion (nm): -0.1773190 ± 0.0367244
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 11.490000 ± 0.255969
Peptide - Tail groups: 10.052500 ± 0.313551
Tilt (°): 85.70510 ± 1.16046
PepDF:
5(ns):  CVS
Displacement (nm): 0.5996030 ± 0.0244713
Precession(°): 0.71739 ± 1.45210
50(ns)  CVS
Displacement (nm): 2.027180 ± 0.120957
Precession(°): 4.86732 ± 5.31914
100(ns)  CVS
Displacement(nm): 3.032870 ± 0.184952
Precession(°): -0.550471 ± 6.322600
200(ns)  CVS
Displacement(nm): 4.042930 ± 0.227055
Precession(°): -11.78200 ± 6.46249

  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.