Trajectory SP1121

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: 45517
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P350 NC01402
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
AVKQPAVVYP
Total charge (e): +1
Number of residues: 10
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 7
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.2
Longitudinal (e nm): 2.05
Transversal (e nm): 0.78
Hydrophobic Dipolar Moment (nm): 1.42
Longitudinal (nm): 1.28
Transversal (nm): 0.6
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): 0.648478000 ± 0.000976131
Upper leaflet (nm2): 0.648478000 ± 0.000976131
Lower leaflet (nm2): 0.648478000 ± 0.000976131
Average Z coordinate
Peptide (nm): 8.434360 ± 0.034576
First Residue (nm): 8.439680 ± 0.041742
Last Residue (nm): 8.351220 ± 0.043581
Membrane (nm): 6.58325000 ± 0.00986729
Upper leaflet Head Group (nm): 8.5528000 ± 0.0114465
Lower leaflet Head Group (nm): 4.61357000 ± 0.00826271
Bilayer Thickness (nm): 3.9392300 ± 0.0141172
Peptide insertion (nm): -0.1184420 ± 0.0364215
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 8.630000 ± 0.291687
Peptide - Tail groups: 7.320000 ± 0.276494
Tilt (°): 90.6222 ± 2.5685
PepDF:
5(ns):  CVS
Displacement (nm): 0.7274260 ± 0.0300017
Precession(°): -2.16912 ± 2.53528
50(ns)  CVS
Displacement (nm): 2.31054 ± 0.11593
Precession(°): -24.11820 ± 7.99221
100(ns)  CVS
Displacement(nm): 3.173850 ± 0.172241
Precession(°): -49.8770 ± 12.1788
200(ns)  CVS
Displacement(nm): 4.595160 ± 0.205057
Precession(°): -108.8810 ± 19.2803

  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.