Trajectory SP658

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: P119 AP00414
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
IGSALKKALPVAKKIGKIALPIAKAALP
Total charge (e): +6
Number of residues: 28
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 21
  Polar: 1
Electrostatic Dipolar Moment (e nm): 7.28
Longitudinal (e nm): 6.79
Transversal (e nm): 2.62
Hydrophobic Dipolar Moment (nm): 3.52
Longitudinal (nm): 3.07
Transversal (nm): 1.74
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): 0.645844000 ± 0.000842656
Upper leaflet (nm2): 0.645844000 ± 0.000842656
Lower leaflet (nm2): 0.645844000 ± 0.000842656
Average Z coordinate
Peptide (nm): 8.4233500 ± 0.0315512
First Residue (nm): 8.5128100 ± 0.0409557
Last Residue (nm): 8.440530 ± 0.051425
Membrane (nm): 6.79671000 ± 0.00874909
Upper leaflet Head Group (nm): 8.7566000 ± 0.0104601
Lower leaflet Head Group (nm): 4.84127000 ± 0.00718275
Bilayer Thickness (nm): 3.9153300 ± 0.0126888
Peptide insertion (nm): -0.3332470 ± 0.0332399
Contacts
Peptide - Water: 29.165000 ± 0.713898
Peptide - Head groups: 15.302500 ± 0.260434
Peptide - Tail groups: 16.105000 ± 0.345868
Tilt (°): 94.011500 ± 0.871437
PepDF:
5(ns):  CVS
Displacement (nm): 0.629918 ± 0.026730
Precession(°): 2.28278 ± 1.31723
50(ns)  CVS
Displacement (nm): 1.9025800 ± 0.0950525
Precession(°): 23.6240 ± 4.4806
100(ns)  CVS
Displacement(nm): 2.746200 ± 0.134904
Precession(°): 47.71080 ± 6.20946
200(ns)  CVS
Displacement(nm): 4.572020 ± 0.234675
Precession(°): 77.95160 ± 8.42192

  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.