Trajectory SP686

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: 19191
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P133 AP01018
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
AFQTFKPDWNKIRYDAMKMQTSLGQMKKRFNL
Total charge (e): +5
Number of residues: 32
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 14
  Polar: 9
Electrostatic Dipolar Moment (e nm): 2.69
Longitudinal (e nm): 2.19
Transversal (e nm): 1.56
Hydrophobic Dipolar Moment (nm): 4.45
Longitudinal (nm): 4.15
Transversal (nm): 1.59
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)
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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): 0.644294000 ± 0.000999185
Upper leaflet (nm2): 0.644294000 ± 0.000999185
Lower leaflet (nm2): 0.644294000 ± 0.000999185
Average Z coordinate
Peptide (nm): 4.6785800 ± 0.0318963
First Residue (nm): 4.7503400 ± 0.0446401
Last Residue (nm): 4.5601900 ± 0.0622677
Membrane (nm): 6.8096700 ± 0.0104452
Upper leaflet Head Group (nm): 8.7656100 ± 0.0124654
Lower leaflet Head Group (nm): 4.85358000 ± 0.00836586
Bilayer Thickness (nm): 3.9120400 ± 0.0150125
Peptide insertion (nm): 0.1749930 ± 0.0329752
Contacts
Peptide - Water: 55.160000 ± 0.931531
Peptide - Head groups: 18.167500 ± 0.296662
Peptide - Tail groups: 14.832500 ± 0.361104
Tilt (°): 90.89300 ± 1.03693
PepDF:
5(ns):  CVS
Displacement (nm): 0.6053000 ± 0.0270573
Precession(°): 1.38631 ± 1.19477
50(ns)  CVS
Displacement (nm): 1.737760 ± 0.100063
Precession(°): 13.50030 ± 4.20974
100(ns)  CVS
Displacement(nm): 2.577490 ± 0.150734
Precession(°): 25.23370 ± 6.55638
200(ns)  CVS
Displacement(nm): 4.094060 ± 0.198081
Precession(°): 47.3929 ± 10.1943

  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.