Trajectory SP850

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: 19195
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P215 NC01525
Lipids: POPC
Heteromolecules:
Ions:
Water model: W

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Sequence :
TLTKAFEQTLLPNSATVL
Total charge (e): 0
Number of residues: 18
By amino acid:
  Basic: 1
  Acidic: 1
  Hydrophobic: 9
  Polar: 7
Electrostatic Dipolar Moment (e nm): 3.41
Longitudinal (e nm): 3.38
Transversal (e nm): 0.47
Hydrophobic Dipolar Moment (nm): 2.06
Longitudinal (nm): 2.02
Transversal (nm): 0.42
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): 0.643509000 ± 0.000963823
Upper leaflet (nm2): 0.643509000 ± 0.000963823
Lower leaflet (nm2): 0.643509000 ± 0.000963823
Average Z coordinate
Peptide (nm): 5.017180 ± 0.032058
First Residue (nm): 4.9205200 ± 0.0436821
Last Residue (nm): 5.012650 ± 0.042298
Membrane (nm): 6.8277600 ± 0.0101447
Upper leaflet Head Group (nm): 8.7869100 ± 0.0119674
Lower leaflet Head Group (nm): 4.86650000 ± 0.00839823
Bilayer Thickness (nm): 3.9204100 ± 0.0146201
Peptide insertion (nm): -0.1506810 ± 0.0331398
Contacts
Peptide - Water: 24.052500 ± 0.618236
Peptide - Head groups: 11.095000 ± 0.230785
Peptide - Tail groups: 10.827500 ± 0.324769
Tilt (°): 89.7568 ± 1.3505
PepDF:
5(ns):  CVS
Displacement (nm): 0.7401860 ± 0.0316116
Precession(°): -1.26541 ± 2.07244
50(ns)  CVS
Displacement (nm): 2.142020 ± 0.108278
Precession(°): -13.96250 ± 6.91759
100(ns)  CVS
Displacement(nm): 2.861370 ± 0.113513
Precession(°): -23.62420 ± 9.65832
200(ns)  CVS
Displacement(nm): 3.349410 ± 0.120629
Precession(°): -35.5432 ± 14.2237

  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.