Trajectory SP959

Force field: martini_v2.2P
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: 45431
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P269 AP01016
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
FFGKMKEYFKKFGASFKRRFANLKKRL
Total charge (e): +9
Number of residues: 27
By amino acid:
  Basic: 10
  Acidic: 1
  Hydrophobic: 13
  Polar: 3
Electrostatic Dipolar Moment (e nm): 2.29
Longitudinal (e nm): 1.87
Transversal (e nm): 1.32
Hydrophobic Dipolar Moment (nm): 7.15
Longitudinal (nm): 6.7
Transversal (nm): 2.51
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): 0.65007400 ± 0.00115856
Upper leaflet (nm2): 0.65007400 ± 0.00115856
Lower leaflet (nm2): 0.65007400 ± 0.00115856
Average Z coordinate
Peptide (nm): 4.530320 ± 0.027942
First Residue (nm): 4.6771100 ± 0.0415136
Last Residue (nm): 4.5787600 ± 0.0352976
Membrane (nm): 6.560400 ± 0.011452
Upper leaflet Head Group (nm): 8.5259200 ± 0.0138924
Lower leaflet Head Group (nm): 4.59260000 ± 0.00919358
Bilayer Thickness (nm): 3.933320 ± 0.016659
Peptide insertion (nm): 0.0622830 ± 0.0294156
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 16.650000 ± 0.284258
Peptide - Tail groups: 15.430000 ± 0.303212
Tilt (°): 88.250200 ± 0.763337
PepDF:
5(ns):  CVS
Displacement (nm): 0.5789940 ± 0.0250395
Precession(°): 0.387697 ± 0.996171
50(ns)  CVS
Displacement (nm): 1.8098200 ± 0.0959917
Precession(°): 3.10348 ± 3.13016
100(ns)  CVS
Displacement(nm): 2.630330 ± 0.139177
Precession(°): 5.10797 ± 4.52210
200(ns)  CVS
Displacement(nm): 3.88023 ± 0.20645
Precession(°): 2.40648 ± 6.42939

  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.