Trajectory SP908

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: 19195
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P244 NC03788
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
GWTLNSAGYLLGKFLPLILRKIVTAL
Total charge (e): +3
Number of residues: 26
By amino acid:
  Basic: 3
  Acidic: 0
  Hydrophobic: 18
  Polar: 5
Electrostatic Dipolar Moment (e nm): 2.87
Longitudinal (e nm): 2.57
Transversal (e nm): 1.28
Hydrophobic Dipolar Moment (nm): 2.36
Longitudinal (nm): 2.18
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): 0.64559400 ± 0.00115705
Upper leaflet (nm2): 0.64559400 ± 0.00115705
Lower leaflet (nm2): 0.64559400 ± 0.00115705
Average Z coordinate
Peptide (nm): 8.3958500 ± 0.0467181
First Residue (nm): 8.6041500 ± 0.0513335
Last Residue (nm): 8.3658300 ± 0.0474416
Membrane (nm): 6.7977900 ± 0.0123233
Upper leaflet Head Group (nm): 8.7589700 ± 0.0147297
Lower leaflet Head Group (nm): 4.84202000 ± 0.00991924
Bilayer Thickness (nm): 3.9169500 ± 0.0177582
Peptide insertion (nm): -0.3631150 ± 0.0489851
Contacts
Peptide - Water: 28.222500 ± 0.911845
Peptide - Head groups: 14.56000 ± 0.26189
Peptide - Tail groups: 16.002500 ± 0.341743
Tilt (°): 90.805300 ± 0.821538
PepDF:
5(ns):  CVS
Displacement (nm): 0.6256020 ± 0.0270454
Precession(°): 0.214821 ± 1.364950
50(ns)  CVS
Displacement (nm): 1.77024 ± 0.09463
Precession(°): 2.08030 ± 3.87256
100(ns)  CVS
Displacement(nm): 2.276400 ± 0.121946
Precession(°): 0.674326 ± 4.477100
200(ns)  CVS
Displacement(nm): 2.281550 ± 0.176255
Precession(°): 0.279339 ± 5.987280

  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.