Trajectory SP674

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: 19193
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P127 AP00955
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
IIRPIIQIIKQKIR
Total charge (e): +4
Number of residues: 14
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.11
Longitudinal (e nm): 1.87
Transversal (e nm): 0.98
Hydrophobic Dipolar Moment (nm): 4.53
Longitudinal (nm): 4.43
Transversal (nm): 0.94
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
 
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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): 0.64338600 ± 0.00100503
Upper leaflet (nm2): 0.64338600 ± 0.00100503
Lower leaflet (nm2): 0.64338600 ± 0.00100503
Average Z coordinate
Peptide (nm): 5.1174200 ± 0.0302369
First Residue (nm): 5.302470 ± 0.037091
Last Residue (nm): 4.9445600 ± 0.0379954
Membrane (nm): 6.8286600 ± 0.0105564
Upper leaflet Head Group (nm): 8.7880000 ± 0.0124617
Lower leaflet Head Group (nm): 4.86640000 ± 0.00871246
Bilayer Thickness (nm): 3.9216000 ± 0.0152053
Peptide insertion (nm): -0.251014 ± 0.031467
Contacts
Peptide - Water: 21.505000 ± 0.577039
Peptide - Head groups: 11.062500 ± 0.246193
Peptide - Tail groups: 9.732500 ± 0.206144
Tilt (°): 85.2645 ± 1.2721
PepDF:
5(ns):  CVS
Displacement (nm): 0.7379920 ± 0.0317385
Precession(°): -2.04859 ± 2.39055
50(ns)  CVS
Displacement (nm): 2.572210 ± 0.107912
Precession(°): -18.86340 ± 8.30142
100(ns)  CVS
Displacement(nm): 3.771940 ± 0.162401
Precession(°): -30.5649 ± 12.1197
200(ns)  CVS
Displacement(nm): 6.041450 ± 0.305693
Precession(°): -62.8870 ± 17.5354

  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.