Trajectory SP746

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: 19190
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P163 AP03031
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
LFSKKGGKGGKSWIKGVFKGIKGIGKEVGGDVIRT-
GIEIAACKIKGEC
Total charge (e): +7
Number of residues: 48
By amino acid:
  Basic: 11
  Acidic: 4
  Hydrophobic: 28
  Polar: 5
Electrostatic Dipolar Moment (e nm): 22.75
Longitudinal (e nm): 22.45
Transversal (e nm): 3.68
Hydrophobic Dipolar Moment (nm): 7.11
Longitudinal (nm): 7.02
Transversal (nm): 1.14
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): 0.647382000 ± 0.000969269
Upper leaflet (nm2): 0.647382000 ± 0.000969269
Lower leaflet (nm2): 0.647382000 ± 0.000969269
Average Z coordinate
Peptide (nm): 8.5478500 ± 0.0355205
First Residue (nm): 8.4989300 ± 0.0396737
Last Residue (nm): 8.8119200 ± 0.0505574
Membrane (nm): 6.77016000 ± 0.00952222
Upper leaflet Head Group (nm): 8.726440 ± 0.011445
Lower leaflet Head Group (nm): 4.81968000 ± 0.00785555
Bilayer Thickness (nm): 3.9067700 ± 0.0138815
Peptide insertion (nm): -0.1785880 ± 0.0373188
Contacts
Peptide - Water: 57.385000 ± 0.912723
Peptide - Head groups: 26.325000 ± 0.371783
Peptide - Tail groups: 24.750000 ± 0.410324
Tilt (°): 88.370100 ± 0.663049
PepDF:
5(ns):  CVS
Displacement (nm): 0.6392440 ± 0.0269833
Precession(°): -0.0939682 ± 0.1971110
50(ns)  CVS
Displacement (nm): 1.8706900 ± 0.0976866
Precession(°): -0.953428 ± 0.494397
100(ns)  CVS
Displacement(nm): 2.451330 ± 0.114321
Precession(°): -1.771870 ± 0.691114
200(ns)  CVS
Displacement(nm): 2.926820 ± 0.107309
Precession(°): -3.168910 ± 0.908945

  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.