Trajectory SP822

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: 19196
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P201 NC00210
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
GIRGNCCMFHTCPIDYSRFYCP
Total charge (e): +1
Number of residues: 22
By amino acid:
  Basic: 5
  Acidic: 1
  Hydrophobic: 9
  Polar: 9
Electrostatic Dipolar Moment (e nm): 5.05
Longitudinal (e nm): 4.93
Transversal (e nm): 1.09
Hydrophobic Dipolar Moment (nm): 2.71
Longitudinal (nm): 2.58
Transversal (nm): 0.84
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): 0.644044000 ± 0.000961292
Upper leaflet (nm2): 0.644044000 ± 0.000961292
Lower leaflet (nm2): 0.644044000 ± 0.000961292
Average Z coordinate
Peptide (nm): 4.9120900 ± 0.0392932
First Residue (nm): 4.8673600 ± 0.0429782
Last Residue (nm): 4.7856100 ± 0.0593381
Membrane (nm): 6.81845000 ± 0.00976051
Upper leaflet Head Group (nm): 8.7756800 ± 0.0119342
Lower leaflet Head Group (nm): 4.85887000 ± 0.00784851
Bilayer Thickness (nm): 3.9168000 ± 0.0142837
Peptide insertion (nm): -0.0532196 ± 0.0400694
Contacts
Peptide - Water: 30.83750 ± 0.81755
Peptide - Head groups: 14.350000 ± 0.270514
Peptide - Tail groups: 12.765000 ± 0.387309
Tilt (°): 89.99860 ± 1.30304
PepDF:
5(ns):  CVS
Displacement (nm): 0.6562170 ± 0.0275499
Precession(°): -1.45232 ± 1.60349
50(ns)  CVS
Displacement (nm): 1.9288500 ± 0.0755859
Precession(°): -12.73330 ± 5.92197
100(ns)  CVS
Displacement(nm): 2.690400 ± 0.129486
Precession(°): -23.00440 ± 9.00586
200(ns)  CVS
Displacement(nm): 3.56641 ± 0.19005
Precession(°): -36.9541 ± 13.8933

  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.