Trajectory SP1123

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: 45481
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P351 NC01521
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
LVVGDQLCYRVLIKCLMNK
Total charge (e): +2
Number of residues: 19
By amino acid:
  Basic: 3
  Acidic: 1
  Hydrophobic: 10
  Polar: 5
Electrostatic Dipolar Moment (e nm): 1.43
Longitudinal (e nm): 0.96
Transversal (e nm): 1.05
Hydrophobic Dipolar Moment (nm): 3.04
Longitudinal (nm): 2.99
Transversal (nm): 0.53
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): 0.64881400 ± 0.00106621
Upper leaflet (nm2): 0.64881400 ± 0.00106621
Lower leaflet (nm2): 0.64881400 ± 0.00106621
Average Z coordinate
Peptide (nm): 4.6060800 ± 0.0440421
First Residue (nm): 4.7925400 ± 0.0406772
Last Residue (nm): 4.514440 ± 0.092569
Membrane (nm): 6.5755300 ± 0.0110118
Upper leaflet Head Group (nm): 8.5433700 ± 0.0132868
Lower leaflet Head Group (nm): 4.6073200 ± 0.0088857
Bilayer Thickness (nm): 3.9360500 ± 0.0159842
Peptide insertion (nm): 0.0012430 ± 0.0449295
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 11.99750 ± 0.24608
Peptide - Tail groups: 10.197500 ± 0.340743
Tilt (°): 82.42770 ± 1.68334
PepDF:
5(ns):  CVS
Displacement (nm): 0.6556070 ± 0.0269264
Precession(°): -1.41451 ± 1.52160
50(ns)  CVS
Displacement (nm): 1.930200 ± 0.101114
Precession(°): -12.9056 ± 5.0104
100(ns)  CVS
Displacement(nm): 2.827480 ± 0.163634
Precession(°): -23.66240 ± 8.15771
200(ns)  CVS
Displacement(nm): 3.616860 ± 0.231946
Precession(°): -39.8765 ± 11.4143

  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.