Trajectory SP1440

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: 19215
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P509 NC02940
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
ANTPCGPYTHDCPVKR
Total charge (e): +1
Number of residues: 16
By amino acid:
  Basic: 5
  Acidic: 1
  Hydrophobic: 6
  Polar: 6
Electrostatic Dipolar Moment (e nm): 1.5
Longitudinal (e nm): 1.16
Transversal (e nm): 0.96
Hydrophobic Dipolar Moment (nm): 1.68
Longitudinal (nm): 1.68
Transversal (nm): 0.04
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): 0.64842000 ± 0.00106811
Upper leaflet (nm2): 0.64842000 ± 0.00106811
Lower leaflet (nm2): 0.64842000 ± 0.00106811
Average Z coordinate
Peptide (nm): 7.66530 ± 1.38122
First Residue (nm): 7.62562 ± 1.31898
Last Residue (nm): 7.70502 ± 1.45225
Membrane (nm): 6.8409300 ± 0.0111186
Upper leaflet Head Group (nm): 8.7842200 ± 0.0132851
Lower leaflet Head Group (nm): 4.89739000 ± 0.00937908
Bilayer Thickness (nm): 3.8868200 ± 0.0162622
Peptide insertion (nm): -1.11892 ± 1.38129
Contacts
Peptide - Water: 63.75750 ± 1.62304
Peptide - Head groups: 1.832500 ± 0.736603
Peptide - Tail groups: 0.375000 ± 0.261571
Tilt (°): 85.43000 ± 6.10672
PepDF:
5(ns):  CVS
Displacement (nm): 1.8031700 ± 0.0897329
Precession(°): -4.32306 ± 14.19090
50(ns)  CVS
Displacement (nm): 5.807420 ± 0.323766
Precession(°): -62.6676 ± 51.2130
100(ns)  CVS
Displacement(nm): 8.816540 ± 0.450706
Precession(°): -150.9880 ± 80.4072
200(ns)  CVS
Displacement(nm): 14.056700 ± 0.619292
Precession(°): -406.881 ± 112.189

  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.