Trajectory SP760

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: 19193
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P170 AP03258
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LPLIAGLFGKIF
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 11
  Polar: 0
Electrostatic Dipolar Moment (e nm): 1.72
Longitudinal (e nm): 1.55
Transversal (e nm): 0.73
Hydrophobic Dipolar Moment (nm): 1.35
Longitudinal (nm): 0.99
Transversal (nm): 0.91
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): 0.643609000 ± 0.000912077
Upper leaflet (nm2): 0.643609000 ± 0.000912077
Lower leaflet (nm2): 0.643609000 ± 0.000912077
Average Z coordinate
Peptide (nm): 5.354740 ± 0.035143
First Residue (nm): 5.3009600 ± 0.0408585
Last Residue (nm): 5.1356400 ± 0.0418655
Membrane (nm): 6.82645000 ± 0.00955364
Upper leaflet Head Group (nm): 8.7857200 ± 0.0112199
Lower leaflet Head Group (nm): 4.86468000 ± 0.00796529
Bilayer Thickness (nm): 3.9210400 ± 0.0137598
Peptide insertion (nm): -0.4900680 ± 0.0360343
Contacts
Peptide - Water: 12.38000 ± 0.49384
Peptide - Head groups: 9.745000 ± 0.237557
Peptide - Tail groups: 10.585000 ± 0.274011
Tilt (°): 84.69410 ± 1.51764
PepDF:
5(ns):  CVS
Displacement (nm): 0.7391170 ± 0.0336583
Precession(°): 2.98437 ± 2.80804
50(ns)  CVS
Displacement (nm): 2.297880 ± 0.109506
Precession(°): 32.36140 ± 9.67183
100(ns)  CVS
Displacement(nm): 3.032060 ± 0.159106
Precession(°): 64.8427 ± 14.2138
200(ns)  CVS
Displacement(nm): 4.534980 ± 0.213585
Precession(°): 140.5560 ± 21.5129

  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.