Trajectory SP965

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: 45491
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P272 AP01223
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
FKDLLKGAAKALVKTVLF
Total charge (e): +3
Number of residues: 18
By amino acid:
  Basic: 4
  Acidic: 1
  Hydrophobic: 12
  Polar: 1
Electrostatic Dipolar Moment (e nm): 3.72
Longitudinal (e nm): 3.55
Transversal (e nm): 1.1
Hydrophobic Dipolar Moment (nm): 4.04
Longitudinal (nm): 3.83
Transversal (nm): 1.31
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): 0.649954000 ± 0.000981359
Upper leaflet (nm2): 0.649954000 ± 0.000981359
Lower leaflet (nm2): 0.649954000 ± 0.000981359
Average Z coordinate
Peptide (nm): 4.8398200 ± 0.0290906
First Residue (nm): 4.7567500 ± 0.0370816
Last Residue (nm): 4.9060300 ± 0.0378798
Membrane (nm): 6.567600 ± 0.010207
Upper leaflet Head Group (nm): 8.5349100 ± 0.0124147
Lower leaflet Head Group (nm): 4.59816000 ± 0.00816826
Bilayer Thickness (nm): 3.9367500 ± 0.0148609
Peptide insertion (nm): -0.2416670 ± 0.0302156
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 12.167500 ± 0.289732
Peptide - Tail groups: 12.472500 ± 0.254625
Tilt (°): 98.81270 ± 1.05176
PepDF:
5(ns):  CVS
Displacement (nm): 0.6234430 ± 0.0262539
Precession(°): 0.79587 ± 1.37960
50(ns)  CVS
Displacement (nm): 1.7957200 ± 0.0945207
Precession(°): 6.50594 ± 5.21105
100(ns)  CVS
Displacement(nm): 2.552220 ± 0.137335
Precession(°): 11.42690 ± 7.70439
200(ns)  CVS
Displacement(nm): 3.295380 ± 0.172444
Precession(°): 8.55491 ± 7.11630

  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.