Trajectory SP756

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: 19196
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P168 AP03200
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
FGHLLRGIVSVGKHIHGLITG
Total charge (e): +2
Number of residues: 21
By amino acid:
  Basic: 11
  Acidic: 0
  Hydrophobic: 14
  Polar: 2
Electrostatic Dipolar Moment (e nm): 4.25
Longitudinal (e nm): 4.03
Transversal (e nm): 1.33
Hydrophobic Dipolar Moment (nm): 2.41
Longitudinal (nm): 1.54
Transversal (nm): 1.85
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: POPC (Healthy mammal)

POPC
2-oleoyl-sn-glycero-3-phosphocholine
Total charge (e): 0

  See POPC lipid
  Download ITP File.
  Download PDB File.
Last snapshot
  Download PDB File.
Total contacts per residue
 
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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): 0.64376800 ± 0.00109805
Upper leaflet (nm2): 0.64376800 ± 0.00109805
Lower leaflet (nm2): 0.64376800 ± 0.00109805
Average Z coordinate
Peptide (nm): 8.592680 ± 0.034081
First Residue (nm): 8.5468500 ± 0.0387962
Last Residue (nm): 8.8547100 ± 0.0459292
Membrane (nm): 6.8209700 ± 0.0111688
Upper leaflet Head Group (nm): 8.7824300 ± 0.0134363
Lower leaflet Head Group (nm): 4.86221000 ± 0.00892391
Bilayer Thickness (nm): 3.9202200 ± 0.0161298
Peptide insertion (nm): -0.189751 ± 0.036634
Contacts
Peptide - Water: 25.832500 ± 0.584291
Peptide - Head groups: 13.635000 ± 0.242559
Peptide - Tail groups: 12.972500 ± 0.280869
Tilt (°): 87.10000 ± 1.05518
PepDF:
5(ns):  CVS
Displacement (nm): 0.668677 ± 0.027320
Precession(°): 0.199901 ± 1.704520
50(ns)  CVS
Displacement (nm): 1.902120 ± 0.089041
Precession(°): 5.13304 ± 4.94076
100(ns)  CVS
Displacement(nm): 2.408730 ± 0.108249
Precession(°): 15.60800 ± 6.92295
200(ns)  CVS
Displacement(nm): 2.875310 ± 0.158486
Precession(°): 33.06830 ± 8.81453

  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.