Trajectory SP971

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: 45512
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P275 AP01447
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
LPGLIAGIAKML
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 11
  Polar: 0
Electrostatic Dipolar Moment (e nm): 1.68
Longitudinal (e nm): 1.55
Transversal (e nm): 0.64
Hydrophobic Dipolar Moment (nm): 1.47
Longitudinal (nm): 0.83
Transversal (nm): 1.21
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): 0.6484980 ± 0.0010282
Upper leaflet (nm2): 0.6484980 ± 0.0010282
Lower leaflet (nm2): 0.6484980 ± 0.0010282
Average Z coordinate
Peptide (nm): 4.8474200 ± 0.0331759
First Residue (nm): 4.8351400 ± 0.0351268
Last Residue (nm): 4.9269100 ± 0.0433203
Membrane (nm): 6.5832600 ± 0.0103411
Upper leaflet Head Group (nm): 8.5526600 ± 0.0122391
Lower leaflet Head Group (nm): 4.61215000 ± 0.00822898
Bilayer Thickness (nm): 3.9405100 ± 0.0147483
Peptide insertion (nm): -0.2352750 ± 0.0341813
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 8.372500 ± 0.228218
Peptide - Tail groups: 8.130000 ± 0.226017
Tilt (°): 92.97290 ± 1.65061
PepDF:
5(ns):  CVS
Displacement (nm): 0.7322470 ± 0.0313008
Precession(°): 0.282809 ± 2.345280
50(ns)  CVS
Displacement (nm): 2.2160800 ± 0.0851835
Precession(°): 2.85536 ± 7.36417
100(ns)  CVS
Displacement(nm): 3.340450 ± 0.117266
Precession(°): 2.75004 ± 10.40350
200(ns)  CVS
Displacement(nm): 4.376830 ± 0.243039
Precession(°): 7.25488 ± 10.17690

  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.