Trajectory SP1113

Force field: martini_v2.2P
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: 45453
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P346 NC00701
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
LPHPVLHMGPLR
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 7
  Acidic: 0
  Hydrophobic: 9
  Polar: 0
Electrostatic Dipolar Moment (e nm): 1.32
Longitudinal (e nm): 1.14
Transversal (e nm): 0.67
Hydrophobic Dipolar Moment (nm): 1.72
Longitudinal (nm): 1.71
Transversal (nm): 0.14
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): 0.64880500 ± 0.00109418
Upper leaflet (nm2): 0.64880500 ± 0.00109418
Lower leaflet (nm2): 0.64880500 ± 0.00109418
Average Z coordinate
Peptide (nm): 4.7526700 ± 0.0396165
First Residue (nm): 4.8323200 ± 0.0413124
Last Residue (nm): 4.5039300 ± 0.0492313
Membrane (nm): 6.5730600 ± 0.0110072
Upper leaflet Head Group (nm): 8.5420600 ± 0.0134729
Lower leaflet Head Group (nm): 4.60322000 ± 0.00863413
Bilayer Thickness (nm): 3.9388400 ± 0.0160021
Peptide insertion (nm): -0.1494510 ± 0.0405465
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 9.895000 ± 0.326581
Peptide - Tail groups: 8.620000 ± 0.291158
Tilt (°): 81.0023 ± 1.8127
PepDF:
5(ns):  CVS
Displacement (nm): 0.7133390 ± 0.0313788
Precession(°): -3.63528 ± 2.03920
50(ns)  CVS
Displacement (nm): 2.0832600 ± 0.0915823
Precession(°): -37.51350 ± 6.07106
100(ns)  CVS
Displacement(nm): 2.923000 ± 0.142038
Precession(°): -77.07040 ± 8.33051
200(ns)  CVS
Displacement(nm): 4.228490 ± 0.197744
Precession(°): -149.5080 ± 10.4659

  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.