Trajectory SP776

Force field: martini_v2.2
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: 19194
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P178 AP03489
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
KRWRRLIFNYF
Total charge (e): +4
Number of residues: 11
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 5
  Polar: 2
Electrostatic Dipolar Moment (e nm): 4.88
Longitudinal (e nm): 4.7
Transversal (e nm): 1.31
Hydrophobic Dipolar Moment (nm): 3.64
Longitudinal (nm): 3.55
Transversal (nm): 0.79
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): 0.642494000 ± 0.000840358
Upper leaflet (nm2): 0.642494000 ± 0.000840358
Lower leaflet (nm2): 0.642494000 ± 0.000840358
Average Z coordinate
Peptide (nm): 4.9636900 ± 0.0282665
First Residue (nm): 4.79964 ± 0.03668
Last Residue (nm): 4.9442000 ± 0.0391685
Membrane (nm): 6.83707000 ± 0.00867158
Upper leaflet Head Group (nm): 8.7980700 ± 0.0102456
Lower leaflet Head Group (nm): 4.87452000 ± 0.00703149
Bilayer Thickness (nm): 3.9235500 ± 0.0124264
Peptide insertion (nm): -0.0891764 ± 0.0291279
Contacts
Peptide - Water: 23.840000 ± 0.581275
Peptide - Head groups: 10.920000 ± 0.256436
Peptide - Tail groups: 9.080000 ± 0.291808
Tilt (°): 90.14270 ± 1.70787
PepDF:
5(ns):  CVS
Displacement (nm): 0.7617670 ± 0.0337499
Precession(°): 3.84007 ± 2.47950
50(ns)  CVS
Displacement (nm): 1.94509 ± 0.10824
Precession(°): 43.17740 ± 8.73087
100(ns)  CVS
Displacement(nm): 2.607250 ± 0.156353
Precession(°): 83.7880 ± 12.2621
200(ns)  CVS
Displacement(nm): 4.362770 ± 0.196297
Precession(°): 166.0090 ± 15.7057

  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.