Trajectory SP1163

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: 45504
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P371 NC02924
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
VKLPPPVKLPPPVKLPPP
Total charge (e): +3
Number of residues: 18
By amino acid:
  Basic: 3
  Acidic: 0
  Hydrophobic: 15
  Polar: 0
Electrostatic Dipolar Moment (e nm): 4.25
Longitudinal (e nm): 4.25
Transversal (e nm): 0.18
Hydrophobic Dipolar Moment (nm): 0.42
Longitudinal (nm): 0.4
Transversal (nm): 0.13
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): 0.64806700 ± 0.00130431
Upper leaflet (nm2): 0.64806700 ± 0.00130431
Lower leaflet (nm2): 0.64806700 ± 0.00130431
Average Z coordinate
Peptide (nm): 6.47078 ± 1.60355
First Residue (nm): 6.42778 ± 1.60901
Last Residue (nm): 6.52626 ± 1.62015
Membrane (nm): 6.5882300 ± 0.0133958
Upper leaflet Head Group (nm): 8.5587500 ± 0.0160392
Lower leaflet Head Group (nm): 4.6183100 ± 0.0104564
Bilayer Thickness (nm): 3.9404400 ± 0.0191466
Peptide insertion (nm): -1.85247 ± 1.60358
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 0.74750 ± 1.47624
Peptide - Tail groups: 0.74750 ± 1.49934
Tilt (°): 90.05920 ± 5.92634
PepDF:
5(ns):  CVS
Displacement (nm): 1.9748800 ± 0.0919551
Precession(°): -2.22692 ± 13.12040
50(ns)  CVS
Displacement (nm): 5.561940 ± 0.294584
Precession(°): -10.8120 ± 43.4594
100(ns)  CVS
Displacement(nm): 7.688130 ± 0.308767
Precession(°): -7.26232 ± 59.98930
200(ns)  CVS
Displacement(nm): 9.054320 ± 0.372273
Precession(°): -14.7835 ± 84.7312

  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.