Trajectory SP670

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: 19191
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P125 AP00890
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
DWKKVDWKKVSKKTCKVMLKACKFLG
Total charge (e): +7
Number of residues: 26
By amino acid:
  Basic: 9
  Acidic: 2
  Hydrophobic: 11
  Polar: 4
Electrostatic Dipolar Moment (e nm): 4.45
Longitudinal (e nm): 4.05
Transversal (e nm): 1.85
Hydrophobic Dipolar Moment (nm): 8.07
Longitudinal (nm): 7.96
Transversal (nm): 1.33
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)
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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): 0.644572000 ± 0.000927343
Upper leaflet (nm2): 0.644572000 ± 0.000927343
Lower leaflet (nm2): 0.644572000 ± 0.000927343
Average Z coordinate
Peptide (nm): 8.7833500 ± 0.0347359
First Residue (nm): 9.110670 ± 0.045747
Last Residue (nm): 8.6780700 ± 0.0456315
Membrane (nm): 6.80608000 ± 0.00949124
Upper leaflet Head Group (nm): 8.7644400 ± 0.0113215
Lower leaflet Head Group (nm): 4.8504400 ± 0.0077657
Bilayer Thickness (nm): 3.9140100 ± 0.0137289
Peptide insertion (nm): 0.0189122 ± 0.0365343
Contacts
Peptide - Water: 41.845000 ± 0.776499
Peptide - Head groups: 16.145000 ± 0.298584
Peptide - Tail groups: 14.385000 ± 0.350898
Tilt (°): 95.931000 ± 0.907712
PepDF:
5(ns):  CVS
Displacement (nm): 0.6446590 ± 0.0259136
Precession(°): 0.17636 ± 1.38615
50(ns)  CVS
Displacement (nm): 1.7253500 ± 0.0918785
Precession(°): 1.33148 ± 4.20843
100(ns)  CVS
Displacement(nm): 2.197010 ± 0.136095
Precession(°): -0.202969 ± 4.430280
200(ns)  CVS
Displacement(nm): 2.678980 ± 0.181183
Precession(°): 5.38128 ± 5.76491

  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.