Trajectory SP1372

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: 19210
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P475 NC00210
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
GIRGNCCMFHTCPIDYSRFYCP
Total charge (e): +1
Number of residues: 22
By amino acid:
  Basic: 5
  Acidic: 1
  Hydrophobic: 9
  Polar: 9
Electrostatic Dipolar Moment (e nm): 5.15
Longitudinal (e nm): 5.04
Transversal (e nm): 1.08
Hydrophobic Dipolar Moment (nm): 2.71
Longitudinal (nm): 2.59
Transversal (nm): 0.8
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): 0.64942500 ± 0.00123538
Upper leaflet (nm2): 0.64942500 ± 0.00123538
Lower leaflet (nm2): 0.64942500 ± 0.00123538
Average Z coordinate
Peptide (nm): 9.0054100 ± 0.0450339
First Residue (nm): 9.1179400 ± 0.0646009
Last Residue (nm): 9.0891500 ± 0.0635175
Membrane (nm): 6.8259000 ± 0.0132782
Upper leaflet Head Group (nm): 8.7663700 ± 0.0158875
Lower leaflet Head Group (nm): 4.8858600 ± 0.0107386
Bilayer Thickness (nm): 3.8805000 ± 0.0191763
Peptide insertion (nm): 0.2390470 ± 0.0477542
Contacts
Peptide - Water: 48.23250 ± 1.37692
Peptide - Head groups: 11.940000 ± 0.321062
Peptide - Tail groups: 9.220000 ± 0.388052
Tilt (°): 94.28230 ± 1.56682
PepDF:
5(ns):  CVS
Displacement (nm): 0.8470860 ± 0.0381098
Precession(°): -1.87725 ± 2.46808
50(ns)  CVS
Displacement (nm): 2.813640 ± 0.154521
Precession(°): -18.79500 ± 7.20615
100(ns)  CVS
Displacement(nm): 4.676740 ± 0.239039
Precession(°): -33.9280 ± 10.4212
200(ns)  CVS
Displacement(nm): 7.326490 ± 0.333706
Precession(°): -55.1226 ± 15.5077

  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.