Trajectory SP832

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: 19189
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P206 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): 5.25
Longitudinal (e nm): 5.17
Transversal (e nm): 0.87
Hydrophobic Dipolar Moment (nm): 1.26
Longitudinal (nm): 1.25
Transversal (nm): 0.21
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): 0.641672000 ± 0.000890236
Upper leaflet (nm2): 0.641672000 ± 0.000890236
Lower leaflet (nm2): 0.641672000 ± 0.000890236
Average Z coordinate
Peptide (nm): 4.185260 ± 0.041175
First Residue (nm): 5.157850 ± 0.039731
Last Residue (nm): 3.0713100 ± 0.0640517
Membrane (nm): 6.84341000 ± 0.00934642
Upper leaflet Head Group (nm): 8.8064200 ± 0.0111295
Lower leaflet Head Group (nm): 4.88022000 ± 0.00760397
Bilayer Thickness (nm): 3.9261900 ± 0.0134791
Peptide insertion (nm): 0.6949670 ± 0.0418713
Contacts
Peptide - Water: 50.707500 ± 0.939437
Peptide - Head groups: 8.477500 ± 0.321733
Peptide - Tail groups: 5.280000 ± 0.253338
Tilt (°): 43.47930 ± 1.86748
PepDF:
5(ns):  CVS
Displacement (nm): 0.8450190 ± 0.0331524
Precession(°): -1.18689 ± 4.27198
50(ns)  CVS
Displacement (nm): 2.31822 ± 0.11353
Precession(°): -14.0924 ± 9.6481
100(ns)  CVS
Displacement(nm): 3.400350 ± 0.168254
Precession(°): -27.7290 ± 12.0852
200(ns)  CVS
Displacement(nm): 4.421130 ± 0.225862
Precession(°): -45.4954 ± 13.0702

  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.