Trajectory SP1216

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: 19204
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P397 AP00542
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
LGTILGLLKSL
Total charge (e): +1
Number of residues: 11
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 1.68
Longitudinal (e nm): 1.55
Transversal (e nm): 0.66
Hydrophobic Dipolar Moment (nm): 1.35
Longitudinal (nm): 0.67
Transversal (nm): 1.18
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): 0.64853800 ± 0.00100597
Upper leaflet (nm2): 0.64853800 ± 0.00100597
Lower leaflet (nm2): 0.64853800 ± 0.00100597
Average Z coordinate
Peptide (nm): 8.7717400 ± 0.0335284
First Residue (nm): 8.707360 ± 0.038128
Last Residue (nm): 8.7943400 ± 0.0433302
Membrane (nm): 6.8402200 ± 0.0105144
Upper leaflet Head Group (nm): 8.7841200 ± 0.0124212
Lower leaflet Head Group (nm): 4.89706000 ± 0.00870862
Bilayer Thickness (nm): 3.8870600 ± 0.0151699
Peptide insertion (nm): -0.0123812 ± 0.0357553
Contacts
Peptide - Water: 19.390000 ± 0.535156
Peptide - Head groups: 7.490000 ± 0.224592
Peptide - Tail groups: 6.657500 ± 0.242198
Tilt (°): 86.53120 ± 1.66994
PepDF:
5(ns):  CVS
Displacement (nm): 0.9265470 ± 0.0392767
Precession(°): 0.803736 ± 4.621540
50(ns)  CVS
Displacement (nm): 2.701470 ± 0.140997
Precession(°): 15.37050 ± 8.73929
100(ns)  CVS
Displacement(nm): 3.984940 ± 0.236905
Precession(°): 29.4282 ± 10.6614
200(ns)  CVS
Displacement(nm): 5.81569 ± 0.42363
Precession(°): 58.4272 ± 15.1329

  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.