Trajectory SP742

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: P161 AP02970
Lipids: POPC
Heteromolecules:
Ions:
Water model: W

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Sequence :
LQHIIGALSHFF
Total charge (e): 0
Number of residues: 12
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 1.74
Longitudinal (e nm): 1.74
Transversal (e nm): 0
Hydrophobic Dipolar Moment (nm): 1.36
Longitudinal (nm): 0.71
Transversal (nm): 1.16
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
 
  Download PDB File.
Contacts per residue
(normalized by number of beads in the residue)
  Download PDB File.

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): 0.642562000 ± 0.000923003
Upper leaflet (nm2): 0.642562000 ± 0.000923003
Lower leaflet (nm2): 0.642562000 ± 0.000923003
Average Z coordinate
Peptide (nm): 8.6463200 ± 0.0351023
First Residue (nm): 8.5672700 ± 0.0408004
Last Residue (nm): 8.7019200 ± 0.0412957
Membrane (nm): 6.83517000 ± 0.00981895
Upper leaflet Head Group (nm): 8.7972900 ± 0.0115563
Lower leaflet Head Group (nm): 4.87414000 ± 0.00786061
Bilayer Thickness (nm): 3.9231400 ± 0.0139763
Peptide insertion (nm): -0.1509700 ± 0.0369556
Contacts
Peptide - Water: 19.115000 ± 0.541753
Peptide - Head groups: 9.912500 ± 0.211608
Peptide - Tail groups: 9.045000 ± 0.218591
Tilt (°): 86.47970 ± 1.34849
PepDF:
5(ns):  CVS
Displacement (nm): 0.7468090 ± 0.0320963
Precession(°): -2.89243 ± 2.82310
50(ns)  CVS
Displacement (nm): 2.282590 ± 0.113482
Precession(°): -23.8267 ± 7.1304
100(ns)  CVS
Displacement(nm): 2.879590 ± 0.135175
Precession(°): -36.6580 ± 8.9136
200(ns)  CVS
Displacement(nm): 3.870350 ± 0.203898
Precession(°): -64.4009 ± 13.1806

  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.