Trajectory SP744

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: 19200
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P162 AP03013
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
NPLKLFLPSTWVHFFKFLR
Total charge (e): +3
Number of residues: 19
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 12
  Polar: 3
Electrostatic Dipolar Moment (e nm): 2.8
Longitudinal (e nm): 2.58
Transversal (e nm): 1.08
Hydrophobic Dipolar Moment (nm): 1.29
Longitudinal (nm): 0.72
Transversal (nm): 1.07
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): 0.644264000 ± 0.000920123
Upper leaflet (nm2): 0.644264000 ± 0.000920123
Lower leaflet (nm2): 0.644264000 ± 0.000920123
Average Z coordinate
Peptide (nm): 8.5673100 ± 0.0351334
First Residue (nm): 8.714760 ± 0.044982
Last Residue (nm): 8.7792300 ± 0.0415088
Membrane (nm): 6.81514000 ± 0.00952055
Upper leaflet Head Group (nm): 8.776530 ± 0.011193
Lower leaflet Head Group (nm): 4.85663000 ± 0.00759558
Bilayer Thickness (nm): 3.9199000 ± 0.0135269
Peptide insertion (nm): -0.2092210 ± 0.0368733
Contacts
Peptide - Water: 27.660000 ± 0.658262
Peptide - Head groups: 13.242500 ± 0.243279
Peptide - Tail groups: 12.822500 ± 0.250047
Tilt (°): 87.826700 ± 0.936997
PepDF:
5(ns):  CVS
Displacement (nm): 0.6825900 ± 0.0285166
Precession(°): -2.33388 ± 1.69344
50(ns)  CVS
Displacement (nm): 2.197110 ± 0.107536
Precession(°): -20.63040 ± 5.32224
100(ns)  CVS
Displacement(nm): 3.347720 ± 0.188013
Precession(°): -34.70450 ± 8.07855
200(ns)  CVS
Displacement(nm): 5.82623 ± 0.24388
Precession(°): -49.4196 ± 12.6226

  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.