Trajectory SP834

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: 19190
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P207 NC00565
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
CWLCNGRCGR
Total charge (e): +2
Number of residues: 10
By amino acid:
  Basic: 2
  Acidic: 0
  Hydrophobic: 4
  Polar: 4
Electrostatic Dipolar Moment (e nm): 1.44
Longitudinal (e nm): 0.79
Transversal (e nm): 1.21
Hydrophobic Dipolar Moment (nm): 3.73
Longitudinal (nm): 3.72
Transversal (nm): 0.35
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): 0.642274000 ± 0.000947644
Upper leaflet (nm2): 0.642274000 ± 0.000947644
Lower leaflet (nm2): 0.642274000 ± 0.000947644
Average Z coordinate
Peptide (nm): 8.69884 ± 0.03556
First Residue (nm): 8.4898400 ± 0.0351365
Last Residue (nm): 9.1287100 ± 0.0447391
Membrane (nm): 6.83899000 ± 0.00960288
Upper leaflet Head Group (nm): 8.8015700 ± 0.0116148
Lower leaflet Head Group (nm): 4.87724000 ± 0.00786395
Bilayer Thickness (nm): 3.9243300 ± 0.0140266
Peptide insertion (nm): -0.1027320 ± 0.0374088
Contacts
Peptide - Water: 18.532500 ± 0.636741
Peptide - Head groups: 9.497500 ± 0.242996
Peptide - Tail groups: 6.962500 ± 0.234129
Tilt (°): 58.83400 ± 2.03846
PepDF:
5(ns):  CVS
Displacement (nm): 0.8083490 ± 0.0340876
Precession(°): 0.403658 ± 3.453840
50(ns)  CVS
Displacement (nm): 2.551620 ± 0.120951
Precession(°): 0.283562 ± 10.458800
100(ns)  CVS
Displacement(nm): 3.585670 ± 0.182568
Precession(°): -9.30163 ± 15.35260
200(ns)  CVS
Displacement(nm): 5.363170 ± 0.208572
Precession(°): -47.6119 ± 20.7916

  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.