Trajectory SP1091

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: 45502
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P335 NC00130
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
LNVPPSWFLSQR
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 7
  Polar: 4
Electrostatic Dipolar Moment (e nm): 1.42
Longitudinal (e nm): 1.22
Transversal (e nm): 0.73
Hydrophobic Dipolar Moment (nm): 1.97
Longitudinal (nm): 1.95
Transversal (nm): 0.31
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): 0.648522000 ± 0.000958919
Upper leaflet (nm2): 0.648522000 ± 0.000958919
Lower leaflet (nm2): 0.648522000 ± 0.000958919
Average Z coordinate
Peptide (nm): 8.5223200 ± 0.0343338
First Residue (nm): 8.2671500 ± 0.0359951
Last Residue (nm): 8.8420400 ± 0.0566376
Membrane (nm): 6.58058000 ± 0.00998184
Upper leaflet Head Group (nm): 8.5509700 ± 0.0117337
Lower leaflet Head Group (nm): 4.61029000 ± 0.00816276
Bilayer Thickness (nm): 3.9406800 ± 0.0142938
Peptide insertion (nm): -0.0286497 ± 0.0362835
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 9.850000 ± 0.235181
Peptide - Tail groups: 8.062500 ± 0.225753
Tilt (°): 70.54440 ± 2.01024
PepDF:
5(ns):  CVS
Displacement (nm): 0.7318060 ± 0.0309029
Precession(°): -1.16695 ± 2.22598
50(ns)  CVS
Displacement (nm): 2.284460 ± 0.111945
Precession(°): -10.65260 ± 6.98418
100(ns)  CVS
Displacement(nm): 3.442630 ± 0.157276
Precession(°): -23.9487 ± 10.6051
200(ns)  CVS
Displacement(nm): 4.528490 ± 0.241412
Precession(°): -34.8690 ± 12.5662

  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.