Trajectory SP1300

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: 19208
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P439 AP03098
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
IVELTLPRVSVRL
Total charge (e): +1
Number of residues: 13
By amino acid:
  Basic: 2
  Acidic: 1
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.15
Longitudinal (e nm): 1.13
Transversal (e nm): 1.83
Hydrophobic Dipolar Moment (nm): 1.71
Longitudinal (nm): 1.64
Transversal (nm): 0.47
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): 0.64836600 ± 0.00109211
Upper leaflet (nm2): 0.64836600 ± 0.00109211
Lower leaflet (nm2): 0.64836600 ± 0.00109211
Average Z coordinate
Peptide (nm): 8.31251 ± 1.66360
First Residue (nm): 8.26062 ± 1.66577
Last Residue (nm): 8.31613 ± 1.65450
Membrane (nm): 6.8412900 ± 0.0114173
Upper leaflet Head Group (nm): 8.7837300 ± 0.0134279
Lower leaflet Head Group (nm): 4.89819000 ± 0.00942868
Bilayer Thickness (nm): 3.8855400 ± 0.0164076
Peptide insertion (nm): -0.471225 ± 1.663660
Contacts
Peptide - Water: 50.73750 ± 4.25225
Peptide - Head groups: 1.93000 ± 1.41392
Peptide - Tail groups: 1.32000 ± 1.07349
Tilt (°): 86.77430 ± 7.46266
PepDF:
5(ns):  CVS
Displacement (nm): 1.913400 ± 0.100732
Precession(°): 0.387466 ± 17.886000
50(ns)  CVS
Displacement (nm): 6.382620 ± 0.305042
Precession(°): 13.7680 ± 60.7944
100(ns)  CVS
Displacement(nm): 8.714720 ± 0.477353
Precession(°): 60.5283 ± 87.3392
200(ns)  CVS
Displacement(nm): 12.829100 ± 0.576546
Precession(°): 285.398 ± 129.934

  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.