Trajectory SP1067

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: 45435
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P323 AP03747
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
WKFGKKLERMGKRIFKATEKGLPVATGVAALARG
Total charge (e): +7
Number of residues: 34
By amino acid:
  Basic: 9
  Acidic: 2
  Hydrophobic: 21
  Polar: 2
Electrostatic Dipolar Moment (e nm): 10.74
Longitudinal (e nm): 10.01
Transversal (e nm): 3.91
Hydrophobic Dipolar Moment (nm): 3.6
Longitudinal (nm): 2.69
Transversal (nm): 2.39
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): 0.650729000 ± 0.000984714
Upper leaflet (nm2): 0.650729000 ± 0.000984714
Lower leaflet (nm2): 0.650729000 ± 0.000984714
Average Z coordinate
Peptide (nm): 8.425380 ± 0.030731
First Residue (nm): 8.5931900 ± 0.0341761
Last Residue (nm): 8.7306200 ± 0.0458051
Membrane (nm): 6.55200000 ± 0.00992591
Upper leaflet Head Group (nm): 8.5195600 ± 0.0117773
Lower leaflet Head Group (nm): 4.5877500 ± 0.0078466
Bilayer Thickness (nm): 3.9318100 ± 0.0141518
Peptide insertion (nm): -0.0941879 ± 0.0329105
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 20.187500 ± 0.332002
Peptide - Tail groups: 18.285000 ± 0.427046
Tilt (°): 89.403400 ± 0.704726
PepDF:
5(ns):  CVS
Displacement (nm): 0.5665910 ± 0.0243413
Precession(°): 0.530690 ± 0.735104
50(ns)  CVS
Displacement (nm): 1.7555200 ± 0.0778431
Precession(°): 6.55297 ± 2.31855
100(ns)  CVS
Displacement(nm): 2.14854 ± 0.10810
Precession(°): 15.37150 ± 3.37817
200(ns)  CVS
Displacement(nm): 3.314520 ± 0.162305
Precession(°): 33.80730 ± 5.36584

  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.