Trajectory SP870

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: P225 NC02346
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
QSCCATPSCARLYEKVY
Total charge (e): +1
Number of residues: 17
By amino acid:
  Basic: 2
  Acidic: 1
  Hydrophobic: 5
  Polar: 9
Electrostatic Dipolar Moment (e nm): 3.09
Longitudinal (e nm): 2.86
Transversal (e nm): 1.18
Hydrophobic Dipolar Moment (nm): 1.02
Longitudinal (nm): 0.59
Transversal (nm): 0.84
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): 0.643541000 ± 0.000898722
Upper leaflet (nm2): 0.643541000 ± 0.000898722
Lower leaflet (nm2): 0.643541000 ± 0.000898722
Average Z coordinate
Peptide (nm): 8.7134100 ± 0.0355493
First Residue (nm): 8.848840 ± 0.045368
Last Residue (nm): 8.6085400 ± 0.0412239
Membrane (nm): 6.82344000 ± 0.00901005
Upper leaflet Head Group (nm): 8.783880 ± 0.010935
Lower leaflet Head Group (nm): 4.86430000 ± 0.00737243
Bilayer Thickness (nm): 3.9195800 ± 0.0131882
Peptide insertion (nm): -0.0704702 ± 0.0371931
Contacts
Peptide - Water: 25.987500 ± 0.644335
Peptide - Head groups: 12.387500 ± 0.259951
Peptide - Tail groups: 10.047500 ± 0.290882
Tilt (°): 99.85930 ± 1.20502
PepDF:
5(ns):  CVS
Displacement (nm): 0.7110080 ± 0.0298719
Precession(°): 0.668432 ± 1.963000
50(ns)  CVS
Displacement (nm): 2.0211800 ± 0.0862186
Precession(°): 5.26517 ± 5.75810
100(ns)  CVS
Displacement(nm): 2.618910 ± 0.124627
Precession(°): 8.85118 ± 6.33130
200(ns)  CVS
Displacement(nm): 3.228990 ± 0.169357
Precession(°): 23.53530 ± 7.17972

  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.