Trajectory SP1133

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: 45481
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P356 NC01995
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
FAKKLAKLAKKLAKLAL
Total charge (e): +6
Number of residues: 17
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 11
  Polar: 0
Electrostatic Dipolar Moment (e nm): 4.53
Longitudinal (e nm): 4.01
Transversal (e nm): 2.11
Hydrophobic Dipolar Moment (nm): 2.38
Longitudinal (nm): 1.58
Transversal (nm): 1.78
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): 0.649105000 ± 0.000941846
Upper leaflet (nm2): 0.649105000 ± 0.000941846
Lower leaflet (nm2): 0.649105000 ± 0.000941846
Average Z coordinate
Peptide (nm): 4.6960800 ± 0.0362389
First Residue (nm): 4.6992900 ± 0.0373317
Last Residue (nm): 4.9382600 ± 0.0500834
Membrane (nm): 6.57423000 ± 0.00902592
Upper leaflet Head Group (nm): 8.5427900 ± 0.0109155
Lower leaflet Head Group (nm): 4.60437000 ± 0.00726616
Bilayer Thickness (nm): 3.9384200 ± 0.0131128
Peptide insertion (nm): -0.0917069 ± 0.0369602
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 10.952500 ± 0.224368
Peptide - Tail groups: 10.987500 ± 0.273631
Tilt (°): 100.21600 ± 1.07922
PepDF:
5(ns):  CVS
Displacement (nm): 0.6348480 ± 0.0283173
Precession(°): -1.12381 ± 1.52711
50(ns)  CVS
Displacement (nm): 1.8534500 ± 0.0960998
Precession(°): -10.3889 ± 4.3512
100(ns)  CVS
Displacement(nm): 2.48620 ± 0.14641
Precession(°): -20.90400 ± 6.14777
200(ns)  CVS
Displacement(nm): 3.535690 ± 0.250638
Precession(°): -40.16550 ± 8.49267

  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.