Trajectory SP666

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: 19193
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P123 AP00542
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LGTILGLLKSL
Total charge (e): +1
Number of residues: 11
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 1.65
Longitudinal (e nm): 1.51
Transversal (e nm): 0.67
Hydrophobic Dipolar Moment (nm): 1.39
Longitudinal (nm): 0.72
Transversal (nm): 1.18
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): 0.64272700 ± 0.00105394
Upper leaflet (nm2): 0.64272700 ± 0.00105394
Lower leaflet (nm2): 0.64272700 ± 0.00105394
Average Z coordinate
Peptide (nm): 8.5374800 ± 0.0433047
First Residue (nm): 8.5114500 ± 0.0448294
Last Residue (nm): 8.4978200 ± 0.0511784
Membrane (nm): 6.8353500 ± 0.0107056
Upper leaflet Head Group (nm): 8.7981000 ± 0.0128024
Lower leaflet Head Group (nm): 4.874230 ± 0.008731
Bilayer Thickness (nm): 3.9238700 ± 0.0154962
Peptide insertion (nm): -0.2606260 ± 0.0451575
Contacts
Peptide - Water: 14.047500 ± 0.405263
Peptide - Head groups: 8.13750 ± 0.22067
Peptide - Tail groups: 7.645000 ± 0.222823
Tilt (°): 90.33010 ± 1.60684
PepDF:
5(ns):  CVS
Displacement (nm): 0.8455220 ± 0.0344757
Precession(°): 1.12311 ± 3.87371
50(ns)  CVS
Displacement (nm): 2.514690 ± 0.129968
Precession(°): 5.70587 ± 13.07880
100(ns)  CVS
Displacement(nm): 3.494890 ± 0.176296
Precession(°): 14.8164 ± 17.6556
200(ns)  CVS
Displacement(nm): 4.799720 ± 0.221896
Precession(°): 47.4912 ± 20.6609

  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.