Trajectory SP862

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: 19194
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P221 NC02046
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
HPTWPQKSVWHGSDPNGRRLTESY
Total charge (e): +1
Number of residues: 24
By amino acid:
  Basic: 9
  Acidic: 2
  Hydrophobic: 9
  Polar: 8
Electrostatic Dipolar Moment (e nm): 5.11
Longitudinal (e nm): 5.09
Transversal (e nm): 0.37
Hydrophobic Dipolar Moment (nm): 5.5
Longitudinal (nm): 5.4
Transversal (nm): 1.05
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)
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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): 0.64341900 ± 0.00115668
Upper leaflet (nm2): 0.64341900 ± 0.00115668
Lower leaflet (nm2): 0.64341900 ± 0.00115668
Average Z coordinate
Peptide (nm): 8.8204500 ± 0.0345518
First Residue (nm): 8.6777500 ± 0.0404703
Last Residue (nm): 8.8259800 ± 0.0501944
Membrane (nm): 6.8212800 ± 0.0119081
Upper leaflet Head Group (nm): 8.7816200 ± 0.0141226
Lower leaflet Head Group (nm): 4.86294000 ± 0.00997209
Bilayer Thickness (nm): 3.9186800 ± 0.0172885
Peptide insertion (nm): 0.0388199 ± 0.0373266
Contacts
Peptide - Water: 37.962500 ± 0.959327
Peptide - Head groups: 15.445000 ± 0.352248
Peptide - Tail groups: 13.672500 ± 0.290422
Tilt (°): 87.65990 ± 0.97321
PepDF:
5(ns):  CVS
Displacement (nm): 0.6634020 ± 0.0296913
Precession(°): -2.35371 ± 1.40335
50(ns)  CVS
Displacement (nm): 2.158970 ± 0.102084
Precession(°): -24.85240 ± 3.66949
100(ns)  CVS
Displacement(nm): 2.834040 ± 0.141515
Precession(°): -53.76150 ± 4.18243
200(ns)  CVS
Displacement(nm): 3.648400 ± 0.233896
Precession(°): -108.16100 ± 4.99232

  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.