Trajectory SP989

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: 45483
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P284 AP02151
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
LYKKLLKKLLKSAKKLG
Total charge (e): +7
Number of residues: 17
By amino acid:
  Basic: 7
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 4.45
Longitudinal (e nm): 3.83
Transversal (e nm): 2.26
Hydrophobic Dipolar Moment (nm): 3.19
Longitudinal (nm): 2.63
Transversal (nm): 1.82
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): 0.64703400 ± 0.00107316
Upper leaflet (nm2): 0.64703400 ± 0.00107316
Lower leaflet (nm2): 0.64703400 ± 0.00107316
Average Z coordinate
Peptide (nm): 6.68925 ± 1.80817
First Residue (nm): 6.70682 ± 1.86018
Last Residue (nm): 6.65671 ± 1.75381
Membrane (nm): 6.5954600 ± 0.0108597
Upper leaflet Head Group (nm): 8.5675300 ± 0.0128355
Lower leaflet Head Group (nm): 4.62314000 ± 0.00895737
Bilayer Thickness (nm): 3.944390 ± 0.015652
Peptide insertion (nm): -1.87828 ± 1.80822
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 0.015000 ± 0.024946
Peptide - Tail groups: 0.0 ± 0.0
Tilt (°): 96.36540 ± 6.43658
PepDF:
5(ns):  CVS
Displacement (nm): 1.9280900 ± 0.0873364
Precession(°): -9.04103 ± 15.32950
50(ns)  CVS
Displacement (nm): 6.000870 ± 0.335357
Precession(°): -122.8500 ± 50.7132
100(ns)  CVS
Displacement(nm): 9.465090 ± 0.502783
Precession(°): -269.8120 ± 86.5913
200(ns)  CVS
Displacement(nm): 13.883800 ± 0.863486
Precession(°): -682.304 ± 157.381

  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.