Trajectory SP904

Force field: martini_v2.2
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: 19195
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P242 NC03705
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
HIQLSPFSQSWR
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 5
  Polar: 5
Electrostatic Dipolar Moment (e nm): 1.37
Longitudinal (e nm): 1.18
Transversal (e nm): 0.7
Hydrophobic Dipolar Moment (nm): 1.34
Longitudinal (nm): 1.21
Transversal (nm): 0.58
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): 0.642145000 ± 0.000876094
Upper leaflet (nm2): 0.642145000 ± 0.000876094
Lower leaflet (nm2): 0.642145000 ± 0.000876094
Average Z coordinate
Peptide (nm): 8.7230900 ± 0.0338079
First Residue (nm): 8.7487500 ± 0.0398844
Last Residue (nm): 9.0260400 ± 0.0471758
Membrane (nm): 6.83999000 ± 0.00954095
Upper leaflet Head Group (nm): 8.8029000 ± 0.0112228
Lower leaflet Head Group (nm): 4.87867000 ± 0.00777202
Bilayer Thickness (nm): 3.9242300 ± 0.0136512
Peptide insertion (nm): -0.079810 ± 0.035622
Contacts
Peptide - Water: 21.942500 ± 0.623637
Peptide - Head groups: 10.17250 ± 0.30359
Peptide - Tail groups: 8.39750 ± 0.31872
Tilt (°): 80.76190 ± 1.90197
PepDF:
5(ns):  CVS
Displacement (nm): 0.7612690 ± 0.0308165
Precession(°): 1.54705 ± 3.10961
50(ns)  CVS
Displacement (nm): 2.545550 ± 0.128261
Precession(°): 15.59560 ± 9.83814
100(ns)  CVS
Displacement(nm): 3.414610 ± 0.170309
Precession(°): 32.6641 ± 13.7963
200(ns)  CVS
Displacement(nm): 5.010140 ± 0.210443
Precession(°): 49.6496 ± 19.0762

  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.