Trajectory SP1093

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: 45453
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P336 NC00188
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
CKRKGSSCRRTSYDCCTGSCRNGKC
Total charge (e): +6
Number of residues: 25
By amino acid:
  Basic: 7
  Acidic: 1
  Hydrophobic: 3
  Polar: 14
Electrostatic Dipolar Moment (e nm): 8.44
Longitudinal (e nm): 8.27
Transversal (e nm): 1.66
Hydrophobic Dipolar Moment (nm): 3.84
Longitudinal (nm): 3.67
Transversal (nm): 1.14
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): 0.64715200 ± 0.00105588
Upper leaflet (nm2): 0.64715200 ± 0.00105588
Lower leaflet (nm2): 0.64715200 ± 0.00105588
Average Z coordinate
Peptide (nm): 6.31707 ± 1.62184
First Residue (nm): 6.36910 ± 1.67078
Last Residue (nm): 6.27571 ± 1.60359
Membrane (nm): 6.5899900 ± 0.0109704
Upper leaflet Head Group (nm): 8.5620100 ± 0.0127404
Lower leaflet Head Group (nm): 4.61812000 ± 0.00910946
Bilayer Thickness (nm): 3.943890 ± 0.015662
Peptide insertion (nm): -1.69895 ± 1.62186
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 0.14250 ± 0.21654
Peptide - Tail groups: 0.0 ± 0.0
Tilt (°): 94.56130 ± 5.80758
PepDF:
5(ns):  CVS
Displacement (nm): 1.751940 ± 0.075398
Precession(°): -0.674851 ± 8.265430
50(ns)  CVS
Displacement (nm): 5.943060 ± 0.308392
Precession(°): 1.77531 ± 30.72270
100(ns)  CVS
Displacement(nm): 9.634830 ± 0.446273
Precession(°): -51.9588 ± 46.4143
200(ns)  CVS
Displacement(nm): 16.016800 ± 0.625741
Precession(°): -213.1270 ± 67.9504

  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.