Trajectory SP1448

Force field: martini_v3
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: 19211
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P513 NC03613
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
ECTRSGGACNSHDQCCANFCRKATSTCM
Total charge (e): +1
Number of residues: 28
By amino acid:
  Basic: 6
  Acidic: 2
  Hydrophobic: 7
  Polar: 15
Electrostatic Dipolar Moment (e nm): 2.76
Longitudinal (e nm): 2.18
Transversal (e nm): 1.7
Hydrophobic Dipolar Moment (nm): 6.48
Longitudinal (nm): 6.25
Transversal (nm): 1.73
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): 0.64810800 ± 0.00114485
Upper leaflet (nm2): 0.64810800 ± 0.00114485
Lower leaflet (nm2): 0.64810800 ± 0.00114485
Average Z coordinate
Peptide (nm): 8.31501 ± 1.61227
First Residue (nm): 8.42823 ± 1.88227
Last Residue (nm): 8.26021 ± 1.43769
Membrane (nm): 6.8371300 ± 0.0119586
Upper leaflet Head Group (nm): 8.7802300 ± 0.0143122
Lower leaflet Head Group (nm): 4.89388000 ± 0.00984839
Bilayer Thickness (nm): 3.8863500 ± 0.0173733
Peptide insertion (nm): -0.465218 ± 1.612330
Contacts
Peptide - Water: 82.55250 ± 7.74177
Peptide - Head groups: 8.45750 ± 2.81774
Peptide - Tail groups: 4.11500 ± 1.64207
Tilt (°): 102.92400 ± 5.57852
PepDF:
5(ns):  CVS
Displacement (nm): 1.1532800 ± 0.0600635
Precession(°): 2.66899 ± 4.07086
50(ns)  CVS
Displacement (nm): 3.615830 ± 0.198005
Precession(°): 25.0159 ± 15.0211
100(ns)  CVS
Displacement(nm): 5.451550 ± 0.340727
Precession(°): 59.2479 ± 20.4980
200(ns)  CVS
Displacement(nm): 8.978330 ± 0.393083
Precession(°): 161.4850 ± 22.5495

  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.