Trajectory SP1053

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: 45504
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P316 AP03517
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
VVNVLVKVLPPPVV
Total charge (e): +1
Number of residues: 14
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 12
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.44
Longitudinal (e nm): 2.37
Transversal (e nm): 0.62
Hydrophobic Dipolar Moment (nm): 0.94
Longitudinal (nm): 0.46
Transversal (nm): 0.83
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)
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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): 0.64905900 ± 0.00113927
Upper leaflet (nm2): 0.64905900 ± 0.00113927
Lower leaflet (nm2): 0.64905900 ± 0.00113927
Average Z coordinate
Peptide (nm): 8.1812300 ± 0.0454575
First Residue (nm): 8.1670700 ± 0.0442562
Last Residue (nm): 8.1470200 ± 0.0655961
Membrane (nm): 6.5752100 ± 0.0116437
Upper leaflet Head Group (nm): 8.5460700 ± 0.0139588
Lower leaflet Head Group (nm): 4.60596000 ± 0.00905952
Bilayer Thickness (nm): 3.940120 ± 0.016641
Peptide insertion (nm): -0.3648400 ± 0.0475524
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 9.005000 ± 0.271273
Peptide - Tail groups: 10.135000 ± 0.238206
Tilt (°): 95.12690 ± 1.85951
PepDF:
5(ns):  CVS
Displacement (nm): 0.6850640 ± 0.0284791
Precession(°): 0.559485 ± 2.130730
50(ns)  CVS
Displacement (nm): 2.126070 ± 0.114438
Precession(°): 7.20983 ± 7.42889
100(ns)  CVS
Displacement(nm): 3.027130 ± 0.151005
Precession(°): 20.87080 ± 7.95805
200(ns)  CVS
Displacement(nm): 4.222840 ± 0.246705
Precession(°): 51.5749 ± 10.5217

  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.