Trajectory SP1228

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: P403 AP01011
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LFGKLIKKFGRKAISYAVKKARGKH
Total charge (e): +9
Number of residues: 25
By amino acid:
  Basic: 12
  Acidic: 0
  Hydrophobic: 13
  Polar: 2
Electrostatic Dipolar Moment (e nm): 5.24
Longitudinal (e nm): 5
Transversal (e nm): 1.54
Hydrophobic Dipolar Moment (nm): 11
Longitudinal (nm): 10.97
Transversal (nm): 0.82
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
 
  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): 0.649364000 ± 0.000978441
Upper leaflet (nm2): 0.649364000 ± 0.000978441
Lower leaflet (nm2): 0.649364000 ± 0.000978441
Average Z coordinate
Peptide (nm): 9.3804500 ± 0.0707418
First Residue (nm): 8.6530500 ± 0.0514376
Last Residue (nm): 10.17860 ± 0.14356
Membrane (nm): 6.8196000 ± 0.0103632
Upper leaflet Head Group (nm): 8.7595200 ± 0.0122703
Lower leaflet Head Group (nm): 4.87941000 ± 0.00854008
Bilayer Thickness (nm): 3.8801100 ± 0.0149497
Peptide insertion (nm): 0.6209320 ± 0.0717981
Contacts
Peptide - Water: 78.38750 ± 2.52476
Peptide - Head groups: 10.06750 ± 0.65368
Peptide - Tail groups: 8.070000 ± 0.620293
Tilt (°): 65.9520 ± 2.8442
PepDF:
5(ns):  CVS
Displacement (nm): 0.852332 ± 0.036824
Precession(°): -0.125408 ± 2.452960
50(ns)  CVS
Displacement (nm): 2.459390 ± 0.126491
Precession(°): 1.25325 ± 7.39791
100(ns)  CVS
Displacement(nm): 3.721980 ± 0.197182
Precession(°): 0.899681 ± 9.657680
200(ns)  CVS
Displacement(nm): 5.163680 ± 0.275351
Precession(°): 9.30625 ± 10.72670

  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.