Trajectory SP1194

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: 19210
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P386 AP00101
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
VQWFSKFLGRIL
Total charge (e): +2
Number of residues: 12
By amino acid:
  Basic: 2
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 1.94
Longitudinal (e nm): 1.64
Transversal (e nm): 1.04
Hydrophobic Dipolar Moment (nm): 1.13
Longitudinal (nm): 0.13
Transversal (nm): 1.12
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): 0.64962700 ± 0.00121683
Upper leaflet (nm2): 0.64962700 ± 0.00121683
Lower leaflet (nm2): 0.64962700 ± 0.00121683
Average Z coordinate
Peptide (nm): 5.0198200 ± 0.0463389
First Residue (nm): 4.8765600 ± 0.0515658
Last Residue (nm): 4.8883000 ± 0.0546473
Membrane (nm): 6.8273100 ± 0.0124427
Upper leaflet Head Group (nm): 8.7683400 ± 0.0146337
Lower leaflet Head Group (nm): 4.8854000 ± 0.0101613
Bilayer Thickness (nm): 3.8829400 ± 0.0178156
Peptide insertion (nm): -0.13442 ± 0.04744
Contacts
Peptide - Water: 24.155000 ± 0.653862
Peptide - Head groups: 8.615000 ± 0.241931
Peptide - Tail groups: 9.365000 ± 0.231804
Tilt (°): 92.04930 ± 1.82272
PepDF:
5(ns):  CVS
Displacement (nm): 0.8409480 ± 0.0323403
Precession(°): 2.81634 ± 3.42616
50(ns)  CVS
Displacement (nm): 2.939030 ± 0.149535
Precession(°): 32.0693 ± 13.0443
100(ns)  CVS
Displacement(nm): 4.41547 ± 0.20988
Precession(°): 63.1076 ± 17.4942
200(ns)  CVS
Displacement(nm): 6.541030 ± 0.286775
Precession(°): 125.6940 ± 24.9107

  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.