Trajectory SP638

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: 19193
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P108 AP00013
Lipids: POPC
Heteromolecules:
Ions:
Water model: W

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Sequence :
LFDIIKKIAESF
Total charge (e): 0
Number of residues: 12
By amino acid:
  Basic: 2
  Acidic: 2
  Hydrophobic: 7
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.11
Longitudinal (e nm): 2.11
Transversal (e nm): 0.08
Hydrophobic Dipolar Moment (nm): 2.41
Longitudinal (nm): 1.85
Transversal (nm): 1.54
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
 
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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): 0.64302300 ± 0.00100665
Upper leaflet (nm2): 0.64302300 ± 0.00100665
Lower leaflet (nm2): 0.64302300 ± 0.00100665
Average Z coordinate
Peptide (nm): 8.6777200 ± 0.0420389
First Residue (nm): 8.5212800 ± 0.0452426
Last Residue (nm): 8.648530 ± 0.048989
Membrane (nm): 6.8321500 ± 0.0105785
Upper leaflet Head Group (nm): 8.7935900 ± 0.0125389
Lower leaflet Head Group (nm): 4.87144000 ± 0.00838194
Bilayer Thickness (nm): 3.9221500 ± 0.0150824
Peptide insertion (nm): -0.115876 ± 0.043869
Contacts
Peptide - Water: 19.347500 ± 0.601894
Peptide - Head groups: 8.915000 ± 0.242151
Peptide - Tail groups: 8.652500 ± 0.203792
Tilt (°): 85.69470 ± 1.37461
PepDF:
5(ns):  CVS
Displacement (nm): 0.784035 ± 0.030432
Precession(°): -1.98080 ± 3.23016
50(ns)  CVS
Displacement (nm): 2.326460 ± 0.115421
Precession(°): -19.7897 ± 11.0128
100(ns)  CVS
Displacement(nm): 3.354070 ± 0.171901
Precession(°): -31.6395 ± 14.4169
200(ns)  CVS
Displacement(nm): 4.601190 ± 0.203832
Precession(°): -91.4047 ± 19.8449

  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.