Trajectory SP880

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: 19192
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P230 NC02461
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
GCTPEYCSMWCKVKVSQNYCVKNCKCPGR
Total charge (e): +4
Number of residues: 29
By amino acid:
  Basic: 5
  Acidic: 1
  Hydrophobic: 9
  Polar: 14
Electrostatic Dipolar Moment (e nm): 2.12
Longitudinal (e nm): 0.14
Transversal (e nm): 2.11
Hydrophobic Dipolar Moment (nm): 7.91
Longitudinal (nm): 7.78
Transversal (nm): 1.45
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
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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): 0.6445840 ± 0.0011316
Upper leaflet (nm2): 0.6445840 ± 0.0011316
Lower leaflet (nm2): 0.6445840 ± 0.0011316
Average Z coordinate
Peptide (nm): 4.8207100 ± 0.0244165
First Residue (nm): 4.7239300 ± 0.0396409
Last Residue (nm): 4.7827400 ± 0.0392147
Membrane (nm): 6.809880 ± 0.011615
Upper leaflet Head Group (nm): 8.7649500 ± 0.0140594
Lower leaflet Head Group (nm): 4.85295000 ± 0.00955296
Bilayer Thickness (nm): 3.9120000 ± 0.0169978
Peptide insertion (nm): 0.0322361 ± 0.0262188
Contacts
Peptide - Water: 42.682500 ± 0.923224
Peptide - Head groups: 17.222500 ± 0.320133
Peptide - Tail groups: 14.215000 ± 0.261563
Tilt (°): 91.692200 ± 0.830759
PepDF:
5(ns):  CVS
Displacement (nm): 0.6357100 ± 0.0283506
Precession(°): -0.655377 ± 1.287900
50(ns)  CVS
Displacement (nm): 1.8778600 ± 0.0928935
Precession(°): -3.51884 ± 4.73543
100(ns)  CVS
Displacement(nm): 2.373760 ± 0.118396
Precession(°): -2.63709 ± 7.10633
200(ns)  CVS
Displacement(nm): 3.821290 ± 0.193592
Precession(°): 6.69441 ± 10.15660

  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.