Trajectory SP1442

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: 19211
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P510 NC03040
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
SPWSQCTASCGGGVQTR
Total charge (e): +1
Number of residues: 17
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 7
  Polar: 9
Electrostatic Dipolar Moment (e nm): 1.58
Longitudinal (e nm): 1.5
Transversal (e nm): 0.49
Hydrophobic Dipolar Moment (nm): 3.77
Longitudinal (nm): 3.55
Transversal (nm): 1.27
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): 0.64832300 ± 0.00129594
Upper leaflet (nm2): 0.64832300 ± 0.00129594
Lower leaflet (nm2): 0.64832300 ± 0.00129594
Average Z coordinate
Peptide (nm): 9.2414300 ± 0.0583944
First Residue (nm): 8.8757700 ± 0.0468826
Last Residue (nm): 9.879700 ± 0.102538
Membrane (nm): 6.8403200 ± 0.0132683
Upper leaflet Head Group (nm): 8.7837700 ± 0.0157828
Lower leaflet Head Group (nm): 4.8974300 ± 0.0106846
Bilayer Thickness (nm): 3.8863400 ± 0.0190593
Peptide insertion (nm): 0.4576600 ± 0.0604897
Contacts
Peptide - Water: 45.282500 ± 0.892762
Peptide - Head groups: 7.775000 ± 0.352892
Peptide - Tail groups: 4.767500 ± 0.235268
Tilt (°): 59.40070 ± 2.62013
PepDF:
5(ns):  CVS
Displacement (nm): 1.0238000 ± 0.0425252
Precession(°): -5.43889 ± 4.98522
50(ns)  CVS
Displacement (nm): 2.789770 ± 0.175692
Precession(°): -58.3882 ± 14.9188
100(ns)  CVS
Displacement(nm): 3.760420 ± 0.200205
Precession(°): -122.8790 ± 21.6912
200(ns)  CVS
Displacement(nm): 4.909630 ± 0.276221
Precession(°): -289.6040 ± 31.2892

  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.