Trajectory SP668

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: 19186
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P124 AP00555
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
GRGKQGGKVRAKAKTRSS
Total charge (e): +7
Number of residues: 18
By amino acid:
  Basic: 7
  Acidic: 0
  Hydrophobic: 7
  Polar: 4
Electrostatic Dipolar Moment (e nm): 5.36
Longitudinal (e nm): 5.36
Transversal (e nm): 0.12
Hydrophobic Dipolar Moment (nm): 0.5
Longitudinal (nm): 0.48
Transversal (nm): 0.14
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): 0.64245400 ± 0.00104634
Upper leaflet (nm2): 0.64245400 ± 0.00104634
Lower leaflet (nm2): 0.64245400 ± 0.00104634
Average Z coordinate
Peptide (nm): 8.9569600 ± 0.0390533
First Residue (nm): 8.8128300 ± 0.0355947
Last Residue (nm): 9.0107900 ± 0.0621833
Membrane (nm): 6.8334000 ± 0.0105848
Upper leaflet Head Group (nm): 8.7942500 ± 0.0125737
Lower leaflet Head Group (nm): 4.87271000 ± 0.00848323
Bilayer Thickness (nm): 3.9215400 ± 0.0151678
Peptide insertion (nm): 0.1627110 ± 0.0410275
Contacts
Peptide - Water: 33.110000 ± 0.943347
Peptide - Head groups: 13.45500 ± 0.31634
Peptide - Tail groups: 7.095000 ± 0.304541
Tilt (°): 80.65280 ± 1.39388
PepDF:
5(ns):  CVS
Displacement (nm): 0.7199140 ± 0.0303845
Precession(°): -0.00732258 ± 1.89598000
50(ns)  CVS
Displacement (nm): 2.377560 ± 0.109868
Precession(°): 0.342032 ± 4.947050
100(ns)  CVS
Displacement(nm): 3.474340 ± 0.154105
Precession(°): 3.90737 ± 6.66306
200(ns)  CVS
Displacement(nm): 4.415540 ± 0.213686
Precession(°): 15.89850 ± 6.24894

  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.