Trajectory SP69

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: 27745
Time step (fs) : 25
Software: GROMACS 2020
Supercomputer: Finisterrae II CESGA
Peptides: P12 DRAMP01549
Lipids: POPC
Heteromolecules:
Ions:
Water model: W

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Sequence :
GLLSVLGSVAKHVLPHVVPVIAEHL
Total charge (e): 0
Number of residues: 25
By amino acid:
  Basic: 4
  Acidic: 1
  Hydrophobic: 18
  Polar: 2
Electrostatic Dipolar Moment (e nm): 6.07
Longitudinal (e nm): 5.96
Transversal (e nm): 1.15
Hydrophobic Dipolar Moment (nm): 10.1
Longitudinal (nm): 9.32
Transversal (nm): 3.76
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
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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): 0.64379 ± 0.00059
Upper leaflet (nm2): 0.64379 ± 0.00059
Lower leaflet (nm2): 0.64379 ± 0.00059
Average Z coordinate
Peptide (nm): 8.346 ± 0.020
First Residue (nm): 8.292 ± 0.026
Last Residue (nm): 8.228 ± 0.026
Membrane (nm): 9.9734 ± 0.0093
Upper leaflet Head Group (nm): 11.933 ± 0.010
Lower leaflet Head Group (nm): 8.0093 ± 0.0081
Bilayer Thickness (nm): 3.924 ± 0.013
Peptide insertion (nm): -0.337 ± 0.022
Contacts
Peptide - Water: 25.00 ± 0.41
Peptide - Head groups: 14.23 ± 0.18
Peptide - Tail groups: 15.06 ± 0.18
Tilt (°): 94.11 ± 0.59
PepDF:
5(ns):  CVS
Displacement (nm): 0.774 ± 0.042
Precession(°): 1.4 ± 2.2
50(ns)  CVS
Displacement (nm): 1.98 ± 0.24
Precession(°): 10.0 ± 15.0
100(ns)  CVS
Displacement(nm): 2.76 ± 0.45
Precession(°): 16.0 ± 22.0
200(ns)  CVS
Displacement(nm): 3.65 ± 0.99
Precession(°): 24.0 ± 34.0

  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.