Trajectory SP1230

Force field: martini_v3
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: 19207
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P404 AP01012
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
WKSMAKKLKEYMEKLKQRA
Total charge (e): +5
Number of residues: 19
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 7
  Polar: 3
Electrostatic Dipolar Moment (e nm): 4.25
Longitudinal (e nm): 4.2
Transversal (e nm): 0.67
Hydrophobic Dipolar Moment (nm): 4.22
Longitudinal (nm): 3.86
Transversal (nm): 1.72
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): 0.64918100 ± 0.00107343
Upper leaflet (nm2): 0.64918100 ± 0.00107343
Lower leaflet (nm2): 0.64918100 ± 0.00107343
Average Z coordinate
Peptide (nm): 9.2089600 ± 0.0610552
First Residue (nm): 8.9173400 ± 0.0528674
Last Residue (nm): 9.414170 ± 0.144312
Membrane (nm): 6.8273700 ± 0.0105002
Upper leaflet Head Group (nm): 8.7666300 ± 0.0126576
Lower leaflet Head Group (nm): 4.88699000 ± 0.00857926
Bilayer Thickness (nm): 3.8796400 ± 0.0152911
Peptide insertion (nm): 0.4423250 ± 0.0623534
Contacts
Peptide - Water: 56.46250 ± 2.14546
Peptide - Head groups: 10.097500 ± 0.471117
Peptide - Tail groups: 7.727500 ± 0.439859
Tilt (°): 78.3239 ± 3.9441
PepDF:
5(ns):  CVS
Displacement (nm): 0.8332510 ± 0.0363498
Precession(°): 2.13486 ± 3.73011
50(ns)  CVS
Displacement (nm): 2.706710 ± 0.121155
Precession(°): 25.35710 ± 7.89902
100(ns)  CVS
Displacement(nm): 3.44466 ± 0.18536
Precession(°): 48.97380 ± 7.91533
200(ns)  CVS
Displacement(nm): 4.450820 ± 0.250623
Precession(°): 93.73600 ± 8.79339

  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.