Trajectory SP1457

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: 17400
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P517 NC03728
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
RGGRLSYSRRRFSTSTGR
Total charge (e): +6
Number of residues: 18
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 5
  Polar: 7
Electrostatic Dipolar Moment (e nm): 5.31
Longitudinal (e nm): 5.16
Transversal (e nm): 1.29
Hydrophobic Dipolar Moment (nm): 0.59
Longitudinal (nm): 0.17
Transversal (nm): 0.57
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): 0.61412400 ± 0.00119185
Upper leaflet (nm2): 0.61412400 ± 0.00119185
Lower leaflet (nm2): 0.61412400 ± 0.00119185
Average Z coordinate
Peptide (nm): 8.792080 ± 0.318684
First Residue (nm): 8.513090 ± 0.284761
Last Residue (nm): 9.092040 ± 0.375421
Membrane (nm): 6.4052100 ± 0.0120076
Upper leaflet Head Group (nm): 8.4176700 ± 0.0140909
Lower leaflet Head Group (nm): 4.39110000 ± 0.00984134
Bilayer Thickness (nm): 4.0265700 ± 0.0171874
Peptide insertion (nm): 0.374411 ± 0.318995
Contacts
Peptide - Water: 54.64500 ± 4.59319
Peptide - Head groups: 9.58750 ± 1.70469
Peptide - Tail groups: 4.805000 ± 0.956102
Tilt (°): 82.27730 ± 4.71574
PepDF:
5(ns):  CVS
Displacement (nm): 0.8882040 ± 0.0466226
Precession(°): 9.58340 ± 4.63196
50(ns)  CVS
Displacement (nm): 2.509660 ± 0.131773
Precession(°): 97.9134 ± 22.1695
100(ns)  CVS
Displacement(nm): 3.33422 ± 0.14648
Precession(°): 204.9990 ± 32.8698
200(ns)  CVS
Displacement(nm): 4.810700 ± 0.267911
Precession(°): 439.1440 ± 54.3322

  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.