Trajectory SP1380

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: 19207
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P479 NC00356
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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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): 2.19
Longitudinal (e nm): 2.04
Transversal (e nm): 0.8
Hydrophobic Dipolar Moment (nm): 1.16
Longitudinal (nm): 1.01
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): 0.64876400 ± 0.00117186
Upper leaflet (nm2): 0.64876400 ± 0.00117186
Lower leaflet (nm2): 0.64876400 ± 0.00117186
Average Z coordinate
Peptide (nm): 5.34730 ± 1.06515
First Residue (nm): 5.30502 ± 1.08101
Last Residue (nm): 5.33358 ± 1.10024
Membrane (nm): 6.8376300 ± 0.0123256
Upper leaflet Head Group (nm): 8.7796400 ± 0.0147117
Lower leaflet Head Group (nm): 4.89560000 ± 0.00998103
Bilayer Thickness (nm): 3.8840400 ± 0.0177779
Peptide insertion (nm): -0.451701 ± 1.065200
Contacts
Peptide - Water: 32.83000 ± 4.45721
Peptide - Head groups: 5.49750 ± 1.38613
Peptide - Tail groups: 4.305 ± 1.175
Tilt (°): 88.93240 ± 5.19791
PepDF:
5(ns):  CVS
Displacement (nm): 1.4326900 ± 0.0928239
Precession(°): 19.6594 ± 11.9331
50(ns)  CVS
Displacement (nm): 5.100630 ± 0.319287
Precession(°): 190.662 ± 36.251
100(ns)  CVS
Displacement(nm): 7.672540 ± 0.421384
Precession(°): 377.4980 ± 51.0367
200(ns)  CVS
Displacement(nm): 10.831600 ± 0.655218
Precession(°): 642.8090 ± 52.9889

  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.