Trajectory SP900

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: 19190
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P240 NC03623
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
QTCCGYRMCIPC
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 4
  Polar: 7
Electrostatic Dipolar Moment (e nm): 2.14
Longitudinal (e nm): 2.03
Transversal (e nm): 0.68
Hydrophobic Dipolar Moment (nm): 2.18
Longitudinal (nm): 2.17
Transversal (nm): 0.2
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): 0.642785000 ± 0.000921549
Upper leaflet (nm2): 0.642785000 ± 0.000921549
Lower leaflet (nm2): 0.642785000 ± 0.000921549
Average Z coordinate
Peptide (nm): 8.6008400 ± 0.0378586
First Residue (nm): 8.9451500 ± 0.0437101
Last Residue (nm): 8.591330 ± 0.045215
Membrane (nm): 6.83300000 ± 0.00947532
Upper leaflet Head Group (nm): 8.7957600 ± 0.0112069
Lower leaflet Head Group (nm): 4.87189000 ± 0.00765279
Bilayer Thickness (nm): 3.9238800 ± 0.0135705
Peptide insertion (nm): -0.1949260 ± 0.0394825
Contacts
Peptide - Water: 17.970000 ± 0.712273
Peptide - Head groups: 8.985000 ± 0.231832
Peptide - Tail groups: 8.57250 ± 0.26123
Tilt (°): 101.78100 ± 1.76222
PepDF:
5(ns):  CVS
Displacement (nm): 0.802116 ± 0.033059
Precession(°): -1.39028 ± 3.10866
50(ns)  CVS
Displacement (nm): 2.640470 ± 0.117066
Precession(°): -19.9314 ± 10.6450
100(ns)  CVS
Displacement(nm): 3.565630 ± 0.177703
Precession(°): -42.6985 ± 14.9560
200(ns)  CVS
Displacement(nm): 3.991280 ± 0.188862
Precession(°): -63.0655 ± 18.2264

  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.