Trajectory SP1402

Force field: martini_v3
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: 19204
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P490 NC01594
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
YGRRARRAARR
Total charge (e): +6
Number of residues: 11
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 4
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.91
Longitudinal (e nm): 2.12
Transversal (e nm): 2
Hydrophobic Dipolar Moment (nm): 1.62
Longitudinal (nm): 1.46
Transversal (nm): 0.69
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): 0.647812000 ± 0.000975046
Upper leaflet (nm2): 0.647812000 ± 0.000975046
Lower leaflet (nm2): 0.647812000 ± 0.000975046
Average Z coordinate
Peptide (nm): 5.53367 ± 1.04570
First Residue (nm): 5.54852 ± 1.01451
Last Residue (nm): 5.51778 ± 1.07959
Membrane (nm): 6.8427300 ± 0.0102465
Upper leaflet Head Group (nm): 8.7870000 ± 0.0121388
Lower leaflet Head Group (nm): 4.89912000 ± 0.00826291
Bilayer Thickness (nm): 3.8878800 ± 0.0146842
Peptide insertion (nm): -0.634544 ± 1.045740
Contacts
Peptide - Water: 61.99250 ± 1.28168
Peptide - Head groups: 0.647500 ± 0.595204
Peptide - Tail groups: 0.225000 ± 0.273528
Tilt (°): 84.96670 ± 8.13599
PepDF:
5(ns):  CVS
Displacement (nm): 1.9549500 ± 0.0851616
Precession(°): 27.6067 ± 24.7519
50(ns)  CVS
Displacement (nm): 6.198550 ± 0.238038
Precession(°): 299.3510 ± 77.3576
100(ns)  CVS
Displacement(nm): 7.998730 ± 0.390242
Precession(°): 594.000 ± 123.085
200(ns)  CVS
Displacement(nm): 9.896200 ± 0.673213
Precession(°): 1195.650 ± 156.367

  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.