Trajectory SP987

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: 45479
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P283 AP02143
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
SLQMGATAIKQVKKLFKKKGG
Total charge (e): +6
Number of residues: 21
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 11
  Polar: 4
Electrostatic Dipolar Moment (e nm): 1.18
Longitudinal (e nm): 0.78
Transversal (e nm): 0.88
Hydrophobic Dipolar Moment (nm): 6.09
Longitudinal (nm): 6.02
Transversal (nm): 0.88
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): 0.64924000 ± 0.00100456
Upper leaflet (nm2): 0.64924000 ± 0.00100456
Lower leaflet (nm2): 0.64924000 ± 0.00100456
Average Z coordinate
Peptide (nm): 8.5534400 ± 0.0392222
First Residue (nm): 8.3494200 ± 0.0459303
Last Residue (nm): 8.7474100 ± 0.0504725
Membrane (nm): 6.5706100 ± 0.0102007
Upper leaflet Head Group (nm): 8.5387500 ± 0.0121787
Lower leaflet Head Group (nm): 4.6037500 ± 0.0080973
Bilayer Thickness (nm): 3.9350000 ± 0.0146249
Peptide insertion (nm): 0.0146923 ± 0.0410695
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 13.167500 ± 0.275623
Peptide - Tail groups: 11.485000 ± 0.347692
Tilt (°): 87.39830 ± 1.08916
PepDF:
5(ns):  CVS
Displacement (nm): 0.5977250 ± 0.0249937
Precession(°): 1.04394 ± 1.32633
50(ns)  CVS
Displacement (nm): 1.7851000 ± 0.0863198
Precession(°): 9.28419 ± 4.62273
100(ns)  CVS
Displacement(nm): 2.41186 ± 0.12870
Precession(°): 19.89670 ± 6.14927
200(ns)  CVS
Displacement(nm): 3.375000 ± 0.196718
Precession(°): 40.22420 ± 7.11543

  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.