Trajectory SP1418

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: 19209
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P498 NC02252
Lipids: POPC
Heteromolecules:
Ions:
Water model: W

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Sequence :
GVDITVIRPNH
Total charge (e): 0
Number of residues: 11
By amino acid:
  Basic: 4
  Acidic: 1
  Hydrophobic: 6
  Polar: 2
Electrostatic Dipolar Moment (e nm): 1.58
Longitudinal (e nm): 1.12
Transversal (e nm): 1.12
Hydrophobic Dipolar Moment (nm): 1.02
Longitudinal (nm): 1.01
Transversal (nm): 0.14
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): 0.648166000 ± 0.000962019
Upper leaflet (nm2): 0.648166000 ± 0.000962019
Lower leaflet (nm2): 0.648166000 ± 0.000962019
Average Z coordinate
Peptide (nm): 7.08800 ± 1.79412
First Residue (nm): 7.06139 ± 1.84271
Last Residue (nm): 7.11046 ± 1.76155
Membrane (nm): 6.8454600 ± 0.0102237
Upper leaflet Head Group (nm): 8.7887600 ± 0.0121368
Lower leaflet Head Group (nm): 4.90170000 ± 0.00823644
Bilayer Thickness (nm): 3.8870600 ± 0.0146677
Peptide insertion (nm): -1.70076 ± 1.79416
Contacts
Peptide - Water: 47.927500 ± 0.882238
Peptide - Head groups: 0.580000 ± 0.383617
Peptide - Tail groups: 0.080000 ± 0.134973
Tilt (°): 94.93280 ± 7.05692
PepDF:
5(ns):  CVS
Displacement (nm): 2.274400 ± 0.109369
Precession(°): 22.3467 ± 24.5302
50(ns)  CVS
Displacement (nm): 6.284610 ± 0.290334
Precession(°): 216.6150 ± 76.0462
100(ns)  CVS
Displacement(nm): 8.984110 ± 0.460762
Precession(°): 526.392 ± 101.549
200(ns)  CVS
Displacement(nm): 13.778200 ± 0.593594
Precession(°): 1100.650 ± 140.109

  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.