Trajectory SP796

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: 19191
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P188 AP03758
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
GLRSLGRKILRAWKKYGPQATPATRQ
Total charge (e): +7
Number of residues: 26
By amino acid:
  Basic: 7
  Acidic: 0
  Hydrophobic: 13
  Polar: 6
Electrostatic Dipolar Moment (e nm): 8.43
Longitudinal (e nm): 7.93
Transversal (e nm): 2.85
Hydrophobic Dipolar Moment (nm): 3.8
Longitudinal (nm): 3.27
Transversal (nm): 1.94
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): 0.644167000 ± 0.000849708
Upper leaflet (nm2): 0.644167000 ± 0.000849708
Lower leaflet (nm2): 0.644167000 ± 0.000849708
Average Z coordinate
Peptide (nm): 8.6781700 ± 0.0278745
First Residue (nm): 8.5378200 ± 0.0422734
Last Residue (nm): 9.1484300 ± 0.0398417
Membrane (nm): 6.8117700 ± 0.0091303
Upper leaflet Head Group (nm): 8.7722400 ± 0.0109401
Lower leaflet Head Group (nm): 4.85410000 ± 0.00711387
Bilayer Thickness (nm): 3.9181400 ± 0.0130497
Peptide insertion (nm): -0.0940763 ± 0.0299445
Contacts
Peptide - Water: 38.232500 ± 0.770826
Peptide - Head groups: 16.575000 ± 0.328481
Peptide - Tail groups: 13.707500 ± 0.265037
Tilt (°): 83.421800 ± 0.844661
PepDF:
5(ns):  CVS
Displacement (nm): 0.6283420 ± 0.0264253
Precession(°): 0.298319 ± 1.371720
50(ns)  CVS
Displacement (nm): 2.064270 ± 0.108274
Precession(°): 3.73961 ± 4.79405
100(ns)  CVS
Displacement(nm): 3.027560 ± 0.147762
Precession(°): 9.15362 ± 7.15568
200(ns)  CVS
Displacement(nm): 4.386410 ± 0.222458
Precession(°): 10.6341 ± 10.5027

  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.