Trajectory SP995

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: 45464
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P287 AP02228
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
KGWFKAMKSIAKFIAKEKLKEHL
Total charge (e): +5
Number of residues: 23
By amino acid:
  Basic: 10
  Acidic: 2
  Hydrophobic: 12
  Polar: 1
Electrostatic Dipolar Moment (e nm): 8.4
Longitudinal (e nm): 7.84
Transversal (e nm): 3
Hydrophobic Dipolar Moment (nm): 2.54
Longitudinal (nm): 2.23
Transversal (nm): 1.22
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): 0.649637000 ± 0.000930288
Upper leaflet (nm2): 0.649637000 ± 0.000930288
Lower leaflet (nm2): 0.649637000 ± 0.000930288
Average Z coordinate
Peptide (nm): 4.5715000 ± 0.0275928
First Residue (nm): 4.503380 ± 0.038167
Last Residue (nm): 4.5543000 ± 0.0471556
Membrane (nm): 6.56804000 ± 0.00920693
Upper leaflet Head Group (nm): 8.5342000 ± 0.0111161
Lower leaflet Head Group (nm): 4.60036000 ± 0.00731464
Bilayer Thickness (nm): 3.9338400 ± 0.0133068
Peptide insertion (nm): 0.0288605 ± 0.0285459
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 15.172500 ± 0.344239
Peptide - Tail groups: 13.887500 ± 0.338995
Tilt (°): 89.5757 ± 1.0583
PepDF:
5(ns):  CVS
Displacement (nm): 0.6033630 ± 0.0251697
Precession(°): 0.333529 ± 0.994579
50(ns)  CVS
Displacement (nm): 1.7751500 ± 0.0721646
Precession(°): 2.32554 ± 3.08589
100(ns)  CVS
Displacement(nm): 2.578920 ± 0.116515
Precession(°): 3.11988 ± 4.53589
200(ns)  CVS
Displacement(nm): 3.220040 ± 0.174822
Precession(°): 3.23279 ± 6.06679

  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.