Trajectory SP1298

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: 19213
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P438 AP03059
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
IVPSIFLLKKAFCIALKKC
Total charge (e): +4
Number of residues: 19
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 12
  Polar: 3
Electrostatic Dipolar Moment (e nm): 2.19
Longitudinal (e nm): 1.91
Transversal (e nm): 1.08
Hydrophobic Dipolar Moment (nm): 4.64
Longitudinal (nm): 4.54
Transversal (nm): 1.01
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): 0.64970500 ± 0.00101151
Upper leaflet (nm2): 0.64970500 ± 0.00101151
Lower leaflet (nm2): 0.64970500 ± 0.00101151
Average Z coordinate
Peptide (nm): 9.0718300 ± 0.0732238
First Residue (nm): 8.6682500 ± 0.0598878
Last Residue (nm): 9.483550 ± 0.225818
Membrane (nm): 6.8241000 ± 0.0106258
Upper leaflet Head Group (nm): 8.7633800 ± 0.0127799
Lower leaflet Head Group (nm): 4.88462000 ± 0.00869002
Bilayer Thickness (nm): 3.8787600 ± 0.0154545
Peptide insertion (nm): 0.3084500 ± 0.0743307
Contacts
Peptide - Water: 45.42250 ± 2.31481
Peptide - Head groups: 9.575000 ± 0.529296
Peptide - Tail groups: 8.090000 ± 0.514318
Tilt (°): 72.28430 ± 6.29172
PepDF:
5(ns):  CVS
Displacement (nm): 0.8425260 ± 0.0340536
Precession(°): 0.215508 ± 3.191590
50(ns)  CVS
Displacement (nm): 2.284950 ± 0.110676
Precession(°): 4.01691 ± 10.98200
100(ns)  CVS
Displacement(nm): 2.915550 ± 0.155846
Precession(°): -6.12567 ± 15.95850
200(ns)  CVS
Displacement(nm): 3.088230 ± 0.184854
Precession(°): -25.2164 ± 24.7419

  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.