Trajectory SP1342

Force field: martini_v3
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: 19211
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P460 AP03747
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
WKFGKKLERMGKRIFKATEKGLPVATGVAALARG
Total charge (e): +7
Number of residues: 34
By amino acid:
  Basic: 9
  Acidic: 2
  Hydrophobic: 21
  Polar: 2
Electrostatic Dipolar Moment (e nm): 11.64
Longitudinal (e nm): 10.85
Transversal (e nm): 4.22
Hydrophobic Dipolar Moment (nm): 3.58
Longitudinal (nm): 2.71
Transversal (nm): 2.34
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)
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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): 0.64985300 ± 0.00123268
Upper leaflet (nm2): 0.64985300 ± 0.00123268
Lower leaflet (nm2): 0.64985300 ± 0.00123268
Average Z coordinate
Peptide (nm): 9.08425 ± 0.13118
First Residue (nm): 9.0018200 ± 0.0556393
Last Residue (nm): 9.480630 ± 0.318438
Membrane (nm): 6.8127800 ± 0.0131503
Upper leaflet Head Group (nm): 8.749420 ± 0.015309
Lower leaflet Head Group (nm): 4.8752500 ± 0.0110039
Bilayer Thickness (nm): 3.8741700 ± 0.0188534
Peptide insertion (nm): 0.33483 ± 0.13207
Contacts
Peptide - Water: 74.65250 ± 6.46322
Peptide - Head groups: 16.63750 ± 1.35637
Peptide - Tail groups: 14.03250 ± 1.56792
Tilt (°): 85.20970 ± 4.26127
PepDF:
5(ns):  CVS
Displacement (nm): 0.709371 ± 0.031287
Precession(°): 0.0685789 ± 1.3723800
50(ns)  CVS
Displacement (nm): 2.009350 ± 0.128662
Precession(°): 1.16332 ± 4.36688
100(ns)  CVS
Displacement(nm): 3.07956 ± 0.19006
Precession(°): 0.526594 ± 6.796820
200(ns)  CVS
Displacement(nm): 4.766250 ± 0.275892
Precession(°): -19.53050 ± 7.92832

  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.