Trajectory SP1105

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: 45516
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P342 NC00356
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
QFRPSYQIPP
Total charge (e): +1
Number of residues: 10
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 5
  Polar: 4
Electrostatic Dipolar Moment (e nm): 2.05
Longitudinal (e nm): 1.9
Transversal (e nm): 0.78
Hydrophobic Dipolar Moment (nm): 1.15
Longitudinal (nm): 1
Transversal (nm): 0.58
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): 0.648251000 ± 0.000971258
Upper leaflet (nm2): 0.648251000 ± 0.000971258
Lower leaflet (nm2): 0.648251000 ± 0.000971258
Average Z coordinate
Peptide (nm): 8.4273900 ± 0.0447942
First Residue (nm): 8.5000200 ± 0.0438782
Last Residue (nm): 8.3380900 ± 0.0626903
Membrane (nm): 6.58457000 ± 0.00939085
Upper leaflet Head Group (nm): 8.5555100 ± 0.0110098
Lower leaflet Head Group (nm): 4.61410000 ± 0.00788145
Bilayer Thickness (nm): 3.94142 ± 0.01354
Peptide insertion (nm): -0.1281190 ± 0.0461274
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 8.722500 ± 0.220626
Peptide - Tail groups: 7.362500 ± 0.321308
Tilt (°): 94.15470 ± 2.68056
PepDF:
5(ns):  CVS
Displacement (nm): 0.7066310 ± 0.0302474
Precession(°): 0.061281 ± 2.490840
50(ns)  CVS
Displacement (nm): 1.9445200 ± 0.0928289
Precession(°): 1.39579 ± 8.42552
100(ns)  CVS
Displacement(nm): 2.669280 ± 0.110786
Precession(°): 4.46572 ± 11.28120
200(ns)  CVS
Displacement(nm): 3.530600 ± 0.185235
Precession(°): 24.0221 ± 12.9854

  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.