Trajectory SP770

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: 19195
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P175 AP03428
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
VDLKKIANILNSIF
Total charge (e): +1
Number of residues: 14
By amino acid:
  Basic: 2
  Acidic: 1
  Hydrophobic: 8
  Polar: 3
Electrostatic Dipolar Moment (e nm): 2.88
Longitudinal (e nm): 2.73
Transversal (e nm): 0.91
Hydrophobic Dipolar Moment (nm): 3.1
Longitudinal (nm): 2.91
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
 
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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): 0.64307300 ± 0.00111963
Upper leaflet (nm2): 0.64307300 ± 0.00111963
Lower leaflet (nm2): 0.64307300 ± 0.00111963
Average Z coordinate
Peptide (nm): 5.0054300 ± 0.0325789
First Residue (nm): 4.9385700 ± 0.0448451
Last Residue (nm): 4.9894900 ± 0.0409495
Membrane (nm): 6.8324100 ± 0.0112962
Upper leaflet Head Group (nm): 8.7924300 ± 0.0136232
Lower leaflet Head Group (nm): 4.87032000 ± 0.00908851
Bilayer Thickness (nm): 3.9221100 ± 0.0163766
Peptide insertion (nm): -0.1351080 ± 0.0338228
Contacts
Peptide - Water: 20.880000 ± 0.577196
Peptide - Head groups: 9.800000 ± 0.228972
Peptide - Tail groups: 9.137500 ± 0.217393
Tilt (°): 85.06560 ± 1.59291
PepDF:
5(ns):  CVS
Displacement (nm): 0.7558290 ± 0.0306137
Precession(°): 2.32444 ± 2.54816
50(ns)  CVS
Displacement (nm): 2.379620 ± 0.111839
Precession(°): 24.8066 ± 9.0571
100(ns)  CVS
Displacement(nm): 3.743850 ± 0.153254
Precession(°): 44.1828 ± 13.3767
200(ns)  CVS
Displacement(nm): 6.233640 ± 0.254277
Precession(°): 102.8090 ± 18.2277

  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.