Trajectory SP1334

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: 19209
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P456 AP03679
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LPLLAGLAANFLPQIICKIARKC
Total charge (e): +3
Number of residues: 23
By amino acid:
  Basic: 3
  Acidic: 0
  Hydrophobic: 16
  Polar: 4
Electrostatic Dipolar Moment (e nm): 1.74
Longitudinal (e nm): 0.82
Transversal (e nm): 1.53
Hydrophobic Dipolar Moment (nm): 6.66
Longitudinal (nm): 6.61
Transversal (nm): 0.8
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): 0.64967200 ± 0.00102985
Upper leaflet (nm2): 0.64967200 ± 0.00102985
Lower leaflet (nm2): 0.64967200 ± 0.00102985
Average Z coordinate
Peptide (nm): 4.721350 ± 0.050129
First Residue (nm): 4.970230 ± 0.051818
Last Residue (nm): 4.467410 ± 0.135779
Membrane (nm): 6.8229300 ± 0.0109972
Upper leaflet Head Group (nm): 8.7624400 ± 0.0132598
Lower leaflet Head Group (nm): 4.88329000 ± 0.00877837
Bilayer Thickness (nm): 3.8791400 ± 0.0159023
Peptide insertion (nm): 0.1619450 ± 0.0508918
Contacts
Peptide - Water: 43.54750 ± 1.72171
Peptide - Head groups: 11.317500 ± 0.401303
Peptide - Tail groups: 10.7275 ± 0.4262
Tilt (°): 80.56030 ± 3.02831
PepDF:
5(ns):  CVS
Displacement (nm): 0.8004890 ± 0.0333971
Precession(°): -5.08956 ± 2.17619
50(ns)  CVS
Displacement (nm): 2.470960 ± 0.116784
Precession(°): -44.35600 ± 6.42871
100(ns)  CVS
Displacement(nm): 3.364290 ± 0.163392
Precession(°): -84.50030 ± 8.63172
200(ns)  CVS
Displacement(nm): 4.231270 ± 0.212476
Precession(°): -158.4060 ± 10.8713

  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.