Trajectory SP1274

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: 19221
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P426 AP02401
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
APIAKYLATALAKWALKQGFAKLKS
Total charge (e): +5
Number of residues: 25
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 16
  Polar: 4
Electrostatic Dipolar Moment (e nm): 2.85
Longitudinal (e nm): 2.8
Transversal (e nm): 0.56
Hydrophobic Dipolar Moment (nm): 5.57
Longitudinal (nm): 5.53
Transversal (nm): 0.69
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
 
  Download PDB File.
Contacts per residue
(normalized by number of beads in the residue)
  Download PDB File.

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): 0.64917400 ± 0.00103772
Upper leaflet (nm2): 0.64917400 ± 0.00103772
Lower leaflet (nm2): 0.64917400 ± 0.00103772
Average Z coordinate
Peptide (nm): 9.206210 ± 0.037399
First Residue (nm): 8.6871100 ± 0.0378484
Last Residue (nm): 9.8910200 ± 0.0727203
Membrane (nm): 6.8269700 ± 0.0108736
Upper leaflet Head Group (nm): 8.7678600 ± 0.0128938
Lower leaflet Head Group (nm): 4.88646000 ± 0.00877215
Bilayer Thickness (nm): 3.8814000 ± 0.0155949
Peptide insertion (nm): 0.4383550 ± 0.0395592
Contacts
Peptide - Water: 64.42250 ± 1.08664
Peptide - Head groups: 10.625000 ± 0.322113
Peptide - Tail groups: 8.950000 ± 0.257849
Tilt (°): 66.15360 ± 1.37152
PepDF:
5(ns):  CVS
Displacement (nm): 0.8199250 ± 0.0332493
Precession(°): 2.82202 ± 2.37538
50(ns)  CVS
Displacement (nm): 2.51430 ± 0.10802
Precession(°): 29.74670 ± 8.50959
100(ns)  CVS
Displacement(nm): 3.475980 ± 0.194751
Precession(°): 56.3495 ± 13.0844
200(ns)  CVS
Displacement(nm): 5.388960 ± 0.319196
Precession(°): 115.6570 ± 21.3314

  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.