Trajectory SP694

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: 19189
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P137 AP01445
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
MGSALRIAAKVLPAALCQIFKKC
Total charge (e): +4
Number of residues: 23
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 15
  Polar: 4
Electrostatic Dipolar Moment (e nm): 3.73
Longitudinal (e nm): 3.6
Transversal (e nm): 0.98
Hydrophobic Dipolar Moment (nm): 1.67
Longitudinal (nm): 1.35
Transversal (nm): 0.98
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): 0.644673000 ± 0.000883772
Upper leaflet (nm2): 0.644673000 ± 0.000883772
Lower leaflet (nm2): 0.644673000 ± 0.000883772
Average Z coordinate
Peptide (nm): 8.5311300 ± 0.0376322
First Residue (nm): 8.5070800 ± 0.0501321
Last Residue (nm): 8.5124800 ± 0.0415125
Membrane (nm): 6.80879000 ± 0.00919446
Upper leaflet Head Group (nm): 8.7700600 ± 0.0108843
Lower leaflet Head Group (nm): 4.85197000 ± 0.00751922
Bilayer Thickness (nm): 3.918090 ± 0.013229
Peptide insertion (nm): -0.2389290 ± 0.0391747
Contacts
Peptide - Water: 27.127500 ± 0.662246
Peptide - Head groups: 13.58750 ± 0.24701
Peptide - Tail groups: 13.612500 ± 0.271953
Tilt (°): 89.9486 ± 0.9736
PepDF:
5(ns):  CVS
Displacement (nm): 0.6626110 ± 0.0276599
Precession(°): -0.943746 ± 1.526730
50(ns)  CVS
Displacement (nm): 1.6241600 ± 0.0787958
Precession(°): -8.82756 ± 4.16504
100(ns)  CVS
Displacement(nm): 1.836020 ± 0.095582
Precession(°): -19.94540 ± 5.95309
200(ns)  CVS
Displacement(nm): 2.483710 ± 0.110964
Precession(°): -51.52800 ± 7.46234

  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.