Trajectory SP1362

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: P470 AP04597
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LWKLIPKAIKKVKSLIKK
Total charge (e): +7
Number of residues: 18
By amino acid:
  Basic: 7
  Acidic: 0
  Hydrophobic: 10
  Polar: 1
Electrostatic Dipolar Moment (e nm): 3.29
Longitudinal (e nm): 2.04
Transversal (e nm): 2.58
Hydrophobic Dipolar Moment (nm): 7.02
Longitudinal (nm): 6.79
Transversal (nm): 1.78
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): 0.64913000 ± 0.00124372
Upper leaflet (nm2): 0.64913000 ± 0.00124372
Lower leaflet (nm2): 0.64913000 ± 0.00124372
Average Z coordinate
Peptide (nm): 8.9921300 ± 0.0433356
First Residue (nm): 8.743340 ± 0.047885
Last Residue (nm): 9.233090 ± 0.061185
Membrane (nm): 6.8268800 ± 0.0125618
Upper leaflet Head Group (nm): 8.7661700 ± 0.0151029
Lower leaflet Head Group (nm): 4.886830 ± 0.010411
Bilayer Thickness (nm): 3.8793300 ± 0.0183436
Peptide insertion (nm): 0.2259650 ± 0.0458919
Contacts
Peptide - Water: 46.34250 ± 0.93548
Peptide - Head groups: 10.98250 ± 0.25563
Peptide - Tail groups: 9.390000 ± 0.243402
Tilt (°): 84.20640 ± 1.37931
PepDF:
5(ns):  CVS
Displacement (nm): 0.7295310 ± 0.0301424
Precession(°): 1.43237 ± 2.41998
50(ns)  CVS
Displacement (nm): 1.9543000 ± 0.0937286
Precession(°): 15.8668 ± 7.9384
100(ns)  CVS
Displacement(nm): 2.517700 ± 0.138152
Precession(°): 31.2138 ± 10.2636
200(ns)  CVS
Displacement(nm): 3.00734 ± 0.19124
Precession(°): 63.3497 ± 12.1802

  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.