Trajectory SP766

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: P173 AP03406
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
WLSKTYKKLENSAKKRIAEGIAIALRGGPR
Total charge (e): +6
Number of residues: 30
By amino acid:
  Basic: 8
  Acidic: 2
  Hydrophobic: 15
  Polar: 5
Electrostatic Dipolar Moment (e nm): 5.67
Longitudinal (e nm): 5.48
Transversal (e nm): 1.48
Hydrophobic Dipolar Moment (nm): 2.32
Longitudinal (nm): 2.21
Transversal (nm): 0.73
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): 0.64486200 ± 0.00117213
Upper leaflet (nm2): 0.64486200 ± 0.00117213
Lower leaflet (nm2): 0.64486200 ± 0.00117213
Average Z coordinate
Peptide (nm): 8.6259300 ± 0.0286159
First Residue (nm): 8.6631000 ± 0.0395283
Last Residue (nm): 8.6927700 ± 0.0470188
Membrane (nm): 6.8043600 ± 0.0120203
Upper leaflet Head Group (nm): 8.7638700 ± 0.0141941
Lower leaflet Head Group (nm): 4.8491600 ± 0.0096642
Bilayer Thickness (nm): 3.9147200 ± 0.0171718
Peptide insertion (nm): -0.1379430 ± 0.0319428
Contacts
Peptide - Water: 40.375000 ± 0.914956
Peptide - Head groups: 18.082500 ± 0.321005
Peptide - Tail groups: 16.722500 ± 0.324926
Tilt (°): 92.072400 ± 0.748332
PepDF:
5(ns):  CVS
Displacement (nm): 0.5886730 ± 0.0242689
Precession(°): 0.351404 ± 1.067560
50(ns)  CVS
Displacement (nm): 1.6604900 ± 0.0674361
Precession(°): 6.07360 ± 3.64178
100(ns)  CVS
Displacement(nm): 2.535100 ± 0.102304
Precession(°): 12.88940 ± 4.53618
200(ns)  CVS
Displacement(nm): 4.01231 ± 0.13781
Precession(°): 28.66780 ± 6.78731

  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.