Trajectory SP1099

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: 45498
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P339 NC00252
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
FAKLLAKLAKKSL
Total charge (e): +4
Number of residues: 13
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 8
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.99
Longitudinal (e nm): 2.46
Transversal (e nm): 1.69
Hydrophobic Dipolar Moment (nm): 2.28
Longitudinal (nm): 2.08
Transversal (nm): 0.93
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): 0.649433000 ± 0.000993602
Upper leaflet (nm2): 0.649433000 ± 0.000993602
Lower leaflet (nm2): 0.649433000 ± 0.000993602
Average Z coordinate
Peptide (nm): 4.7390900 ± 0.0302601
First Residue (nm): 4.760030 ± 0.037488
Last Residue (nm): 4.8411900 ± 0.0538953
Membrane (nm): 6.5732100 ± 0.0102269
Upper leaflet Head Group (nm): 8.5410900 ± 0.0122763
Lower leaflet Head Group (nm): 4.60383000 ± 0.00808921
Bilayer Thickness (nm): 3.9372600 ± 0.0147018
Peptide insertion (nm): -0.1352610 ± 0.0313226
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 9.282500 ± 0.232204
Peptide - Tail groups: 9.202500 ± 0.232087
Tilt (°): 97.02060 ± 1.59925
PepDF:
5(ns):  CVS
Displacement (nm): 0.6835890 ± 0.0281482
Precession(°): 2.02312 ± 2.04469
50(ns)  CVS
Displacement (nm): 2.06077 ± 0.10653
Precession(°): 23.07580 ± 6.53417
100(ns)  CVS
Displacement(nm): 3.114150 ± 0.142317
Precession(°): 47.96410 ± 8.75542
200(ns)  CVS
Displacement(nm): 4.679970 ± 0.225768
Precession(°): 79.39040 ± 8.80694

  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.