Trajectory SP1414

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: 19212
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P496 NC02053
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
STNITVTLKKFPL
Total charge (e): +2
Number of residues: 13
By amino acid:
  Basic: 2
  Acidic: 0
  Hydrophobic: 6
  Polar: 5
Electrostatic Dipolar Moment (e nm): 1.94
Longitudinal (e nm): 1.78
Transversal (e nm): 0.77
Hydrophobic Dipolar Moment (nm): 2.05
Longitudinal (nm): 1.83
Transversal (nm): 0.92
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
 
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Contacts per residue
(normalized by number of beads in the residue)
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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): 0.64894900 ± 0.00111399
Upper leaflet (nm2): 0.64894900 ± 0.00111399
Lower leaflet (nm2): 0.64894900 ± 0.00111399
Average Z coordinate
Peptide (nm): 7.03248 ± 1.46683
First Residue (nm): 7.04357 ± 1.61472
Last Residue (nm): 7.03817 ± 1.43466
Membrane (nm): 6.8359500 ± 0.0114472
Upper leaflet Head Group (nm): 8.7775500 ± 0.0134734
Lower leaflet Head Group (nm): 4.89426000 ± 0.00944734
Bilayer Thickness (nm): 3.8832900 ± 0.0164556
Peptide insertion (nm): -1.74507 ± 1.46690
Contacts
Peptide - Water: 31.48500 ± 3.25334
Peptide - Head groups: 7.602500 ± 0.891824
Peptide - Tail groups: 6.675000 ± 0.902625
Tilt (°): 103.146 ± 2.669
PepDF:
5(ns):  CVS
Displacement (nm): 0.9829380 ± 0.0505945
Precession(°): -2.12058 ± 5.87662
50(ns)  CVS
Displacement (nm): 3.105160 ± 0.219783
Precession(°): -22.2608 ± 18.6047
100(ns)  CVS
Displacement(nm): 4.824760 ± 0.377317
Precession(°): -35.2139 ± 21.4534
200(ns)  CVS
Displacement(nm): 8.385270 ± 0.657671
Precession(°): -77.5976 ± 29.2634

  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.