Trajectory SP1085

Force field: martini_v2.2P
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: 45487
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P332 AP04269
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
ILGKLWKGVKSIF
Total charge (e): +3
Number of residues: 13
By amino acid:
  Basic: 3
  Acidic: 0
  Hydrophobic: 9
  Polar: 1
Electrostatic Dipolar Moment (e nm): 3.27
Longitudinal (e nm): 2.98
Transversal (e nm): 1.33
Hydrophobic Dipolar Moment (nm): 1.59
Longitudinal (nm): 0.49
Transversal (nm): 1.51
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): 0.649355000 ± 0.000977653
Upper leaflet (nm2): 0.649355000 ± 0.000977653
Lower leaflet (nm2): 0.649355000 ± 0.000977653
Average Z coordinate
Peptide (nm): 8.3999600 ± 0.0396805
First Residue (nm): 8.1959700 ± 0.0430177
Last Residue (nm): 8.3829300 ± 0.0532153
Membrane (nm): 6.57102000 ± 0.00993378
Upper leaflet Head Group (nm): 8.5404400 ± 0.0117909
Lower leaflet Head Group (nm): 4.60256000 ± 0.00817396
Bilayer Thickness (nm): 3.9378900 ± 0.0143471
Peptide insertion (nm): -0.1404810 ± 0.0413952
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 9.85750 ± 0.30336
Peptide - Tail groups: 9.652500 ± 0.236322
Tilt (°): 84.56550 ± 1.84462
PepDF:
5(ns):  CVS
Displacement (nm): 0.6843400 ± 0.0305742
Precession(°): -0.400105 ± 1.977270
50(ns)  CVS
Displacement (nm): 2.281830 ± 0.105299
Precession(°): -3.86632 ± 6.22530
100(ns)  CVS
Displacement(nm): 3.515430 ± 0.151526
Precession(°): -11.95910 ± 7.69079
200(ns)  CVS
Displacement(nm): 5.458670 ± 0.220029
Precession(°): -6.58520 ± 9.39443

  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.