Trajectory SP644

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: 19198
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P112 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): 1.96
Longitudinal (e nm): 1.63
Transversal (e nm): 1.07
Hydrophobic Dipolar Moment (nm): 1.18
Longitudinal (nm): 0.17
Transversal (nm): 1.17
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): 0.64343700 ± 0.00112503
Upper leaflet (nm2): 0.64343700 ± 0.00112503
Lower leaflet (nm2): 0.64343700 ± 0.00112503
Average Z coordinate
Peptide (nm): 8.4270100 ± 0.0408256
First Residue (nm): 8.5785600 ± 0.0413359
Last Residue (nm): 8.4314200 ± 0.0425998
Membrane (nm): 6.8280800 ± 0.0118793
Upper leaflet Head Group (nm): 8.7910300 ± 0.0141274
Lower leaflet Head Group (nm): 4.86764000 ± 0.00961033
Bilayer Thickness (nm): 3.9234000 ± 0.0170863
Peptide insertion (nm): -0.3640270 ± 0.0432008
Contacts
Peptide - Water: 17.475000 ± 0.611069
Peptide - Head groups: 9.580000 ± 0.225078
Peptide - Tail groups: 10.16750 ± 0.24624
Tilt (°): 96.29630 ± 1.23205
PepDF:
5(ns):  CVS
Displacement (nm): 0.7451420 ± 0.0323717
Precession(°): 6.85759 ± 2.57884
50(ns)  CVS
Displacement (nm): 2.363280 ± 0.118288
Precession(°): 65.81920 ± 7.55481
100(ns)  CVS
Displacement(nm): 3.344490 ± 0.155232
Precession(°): 137.0380 ± 11.0852
200(ns)  CVS
Displacement(nm): 4.899660 ± 0.210404
Precession(°): 296.0470 ± 14.8751

  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.