Trajectory SP882

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: 19192
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P231 NC02533
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
SATGAPWKMWVR
Total charge (e): +2
Number of residues: 12
By amino acid:
  Basic: 2
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.04
Longitudinal (e nm): 1.52
Transversal (e nm): 1.35
Hydrophobic Dipolar Moment (nm): 1.72
Longitudinal (nm): 1.37
Transversal (nm): 1.04
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): 0.64301200 ± 0.00086117
Upper leaflet (nm2): 0.64301200 ± 0.00086117
Lower leaflet (nm2): 0.64301200 ± 0.00086117
Average Z coordinate
Peptide (nm): 8.5491900 ± 0.0411745
First Residue (nm): 8.7032300 ± 0.0450313
Last Residue (nm): 8.7865200 ± 0.0473074
Membrane (nm): 6.83013000 ± 0.00899613
Upper leaflet Head Group (nm): 8.7915600 ± 0.0108421
Lower leaflet Head Group (nm): 4.87013000 ± 0.00747068
Bilayer Thickness (nm): 3.9214200 ± 0.0131667
Peptide insertion (nm): -0.2423680 ± 0.0425781
Contacts
Peptide - Water: 18.617500 ± 0.643251
Peptide - Head groups: 9.817500 ± 0.267226
Peptide - Tail groups: 8.877500 ± 0.241807
Tilt (°): 87.37610 ± 1.68868
PepDF:
5(ns):  CVS
Displacement (nm): 0.7854380 ± 0.0337634
Precession(°): 0.48550 ± 2.65429
50(ns)  CVS
Displacement (nm): 2.233950 ± 0.107864
Precession(°): 0.161607 ± 8.284980
100(ns)  CVS
Displacement(nm): 3.01272 ± 0.13320
Precession(°): -0.652278 ± 10.833400
200(ns)  CVS
Displacement(nm): 4.979170 ± 0.197033
Precession(°): 11.5705 ± 14.4857

  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.