Trajectory SP1288

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: 19223
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P433 AP02895
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
MATPHVAGAAALILSKHPTWTNAQVRDRLESTATY-
LGNSFYYGK
Total charge (e): +2
Number of residues: 44
By amino acid:
  Basic: 10
  Acidic: 2
  Hydrophobic: 22
  Polar: 14
Electrostatic Dipolar Moment (e nm): 6.52
Longitudinal (e nm): 6.48
Transversal (e nm): 0.73
Hydrophobic Dipolar Moment (nm): 10.91
Longitudinal (nm): 10.91
Transversal (nm): 0.24
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): 0.650040000 ± 0.000913968
Upper leaflet (nm2): 0.650040000 ± 0.000913968
Lower leaflet (nm2): 0.650040000 ± 0.000913968
Average Z coordinate
Peptide (nm): 9.215790 ± 0.163346
First Residue (nm): 8.8101300 ± 0.0713975
Last Residue (nm): 9.797780 ± 0.470849
Membrane (nm): 6.81199000 ± 0.00924396
Upper leaflet Head Group (nm): 8.7501000 ± 0.0111251
Lower leaflet Head Group (nm): 4.87327000 ± 0.00753362
Bilayer Thickness (nm): 3.8768300 ± 0.0134359
Peptide insertion (nm): 0.465684 ± 0.163724
Contacts
Peptide - Water: 94.11750 ± 9.37929
Peptide - Head groups: 19.08000 ± 1.94516
Peptide - Tail groups: 14.94750 ± 2.31444
Tilt (°): 82.3176 ± 4.7043
PepDF:
5(ns):  CVS
Displacement (nm): 0.7483570 ± 0.0281062
Precession(°): 10.7900 ± 10.9611
50(ns)  CVS
Displacement (nm): 2.0241000 ± 0.0994038
Precession(°): 113.3010 ± 51.8451
100(ns)  CVS
Displacement(nm): 2.800820 ± 0.141791
Precession(°): 243.1890 ± 79.0492
200(ns)  CVS
Displacement(nm): 4.708600 ± 0.216113
Precession(°): 676.671 ± 106.431

  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.