Trajectory SP1382

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: 19209
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P480 NC00415
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
PGLKGKRGDSGSPATWTTRG
Total charge (e): +3
Number of residues: 20
By amino acid:
  Basic: 4
  Acidic: 1
  Hydrophobic: 10
  Polar: 5
Electrostatic Dipolar Moment (e nm): 5.37
Longitudinal (e nm): 5.29
Transversal (e nm): 0.9
Hydrophobic Dipolar Moment (nm): 1.28
Longitudinal (nm): 1.26
Transversal (nm): 0.22
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
 
  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): 0.648009000 ± 0.000970671
Upper leaflet (nm2): 0.648009000 ± 0.000970671
Lower leaflet (nm2): 0.648009000 ± 0.000970671
Average Z coordinate
Peptide (nm): 6.21026 ± 2.09580
First Residue (nm): 6.33283 ± 2.19573
Last Residue (nm): 6.06933 ± 2.03186
Membrane (nm): 6.8408500 ± 0.0104548
Upper leaflet Head Group (nm): 8.7847100 ± 0.0125822
Lower leaflet Head Group (nm): 4.89696000 ± 0.00846276
Bilayer Thickness (nm): 3.8877500 ± 0.0151634
Peptide insertion (nm): -1.31330 ± 2.09582
Contacts
Peptide - Water: 70.38250 ± 4.61343
Peptide - Head groups: 4.13250 ± 1.79027
Peptide - Tail groups: 1.652500 ± 0.936248
Tilt (°): 92.8685 ± 10.3497
PepDF:
5(ns):  CVS
Displacement (nm): 1.4572900 ± 0.0815652
Precession(°): -5.44813 ± 10.05270
50(ns)  CVS
Displacement (nm): 5.094740 ± 0.279554
Precession(°): -60.7900 ± 33.8307
100(ns)  CVS
Displacement(nm): 6.503310 ± 0.291589
Precession(°): -133.1520 ± 52.7531
200(ns)  CVS
Displacement(nm): 6.913100 ± 0.392382
Precession(°): -312.9730 ± 64.6615

  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.