Trajectory SP854

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: 19191
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P217 NC01730
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
GRRINRLILPRN
Total charge (e): +4
Number of residues: 12
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 6
  Polar: 2
Electrostatic Dipolar Moment (e nm): 3.71
Longitudinal (e nm): 3.58
Transversal (e nm): 1
Hydrophobic Dipolar Moment (nm): 1.37
Longitudinal (nm): 1.2
Transversal (nm): 0.66
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): 0.642374000 ± 0.000907235
Upper leaflet (nm2): 0.642374000 ± 0.000907235
Lower leaflet (nm2): 0.642374000 ± 0.000907235
Average Z coordinate
Peptide (nm): 8.8693100 ± 0.0395047
First Residue (nm): 8.8167500 ± 0.0603417
Last Residue (nm): 8.9094200 ± 0.0474675
Membrane (nm): 6.83752000 ± 0.00968293
Upper leaflet Head Group (nm): 8.798970 ± 0.011592
Lower leaflet Head Group (nm): 4.87640000 ± 0.00790308
Bilayer Thickness (nm): 3.9225700 ± 0.0140298
Peptide insertion (nm): 0.0703380 ± 0.0411703
Contacts
Peptide - Water: 25.020000 ± 0.656439
Peptide - Head groups: 10.215000 ± 0.227398
Peptide - Tail groups: 6.355000 ± 0.227471
Tilt (°): 87.66040 ± 1.83813
PepDF:
5(ns):  CVS
Displacement (nm): 0.7506740 ± 0.0305588
Precession(°): -2.08666 ± 2.65310
50(ns)  CVS
Displacement (nm): 1.9862700 ± 0.0958434
Precession(°): -24.03750 ± 9.19058
100(ns)  CVS
Displacement(nm): 2.48376 ± 0.14392
Precession(°): -51.6176 ± 11.5367
200(ns)  CVS
Displacement(nm): 3.597580 ± 0.227261
Precession(°): -111.6730 ± 13.6831

  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.