Trajectory SP639

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: 45503
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P109 AP00013
Lipids: POPC
Heteromolecules:
Ions:
Water model: PW

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Sequence :
LFDIIKKIAESF
Total charge (e): 0
Number of residues: 12
By amino acid:
  Basic: 2
  Acidic: 2
  Hydrophobic: 7
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.1
Longitudinal (e nm): 2.1
Transversal (e nm): 0.06
Hydrophobic Dipolar Moment (nm): 2.41
Longitudinal (nm): 1.85
Transversal (nm): 1.54
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
 
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Contacts per residue
(normalized by number of beads in the residue)
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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): 0.64811900 ± 0.00114472
Upper leaflet (nm2): 0.64811900 ± 0.00114472
Lower leaflet (nm2): 0.64811900 ± 0.00114472
Average Z coordinate
Peptide (nm): 4.5960700 ± 0.0410685
First Residue (nm): 4.8317400 ± 0.0493968
Last Residue (nm): 4.6992800 ± 0.0446881
Membrane (nm): 6.5848000 ± 0.0110648
Upper leaflet Head Group (nm): 8.5554400 ± 0.0131267
Lower leaflet Head Group (nm): 4.61452000 ± 0.00905949
Bilayer Thickness (nm): 3.9409200 ± 0.0159495
Peptide insertion (nm): 0.0184516 ± 0.0420559
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 8.870000 ± 0.212888
Peptide - Tail groups: 8.152500 ± 0.238179
Tilt (°): 85.45010 ± 1.57783
PepDF:
5(ns):  CVS
Displacement (nm): 0.6870060 ± 0.0294556
Precession(°): -2.27862 ± 2.20634
50(ns)  CVS
Displacement (nm): 2.1024200 ± 0.0966709
Precession(°): -25.43870 ± 5.68741
100(ns)  CVS
Displacement(nm): 2.771990 ± 0.149634
Precession(°): -49.5452 ± 7.2819
200(ns)  CVS
Displacement(nm): 3.662520 ± 0.211787
Precession(°): -104.35600 ± 9.74527

  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.