Trajectory SP662

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: 19187
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P121 AP00492
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
QRVEELSKFSKKGAAARRRK
Total charge (e): +6
Number of residues: 20
By amino acid:
  Basic: 8
  Acidic: 2
  Hydrophobic: 7
  Polar: 3
Electrostatic Dipolar Moment (e nm): 0.74
Longitudinal (e nm): 0.52
Transversal (e nm): 0.53
Hydrophobic Dipolar Moment (nm): 4.72
Longitudinal (nm): 4.51
Transversal (nm): 1.38
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): 0.641299000 ± 0.000991549
Upper leaflet (nm2): 0.641299000 ± 0.000991549
Lower leaflet (nm2): 0.641299000 ± 0.000991549
Average Z coordinate
Peptide (nm): 8.04868 ± 2.11283
First Residue (nm): 8.12515 ± 2.08889
Last Residue (nm): 7.97494 ± 2.14430
Membrane (nm): 6.8456000 ± 0.0106927
Upper leaflet Head Group (nm): 8.8090800 ± 0.0128163
Lower leaflet Head Group (nm): 4.88259000 ± 0.00867147
Bilayer Thickness (nm): 3.9265000 ± 0.0154743
Peptide insertion (nm): -0.760405 ± 2.112870
Contacts
Peptide - Water: 87.775000 ± 0.780095
Peptide - Head groups: 0.140000 ± 0.129704
Peptide - Tail groups: 0.0 ± 0.0
Tilt (°): 88.17090 ± 7.67427
PepDF:
5(ns):  CVS
Displacement (nm): 1.5095300 ± 0.0682761
Precession(°): -3.2064 ± 10.2967
50(ns)  CVS
Displacement (nm): 5.230460 ± 0.242786
Precession(°): -48.0580 ± 36.9171
100(ns)  CVS
Displacement(nm): 7.959270 ± 0.368614
Precession(°): -98.1761 ± 51.1337
200(ns)  CVS
Displacement(nm): 11.246700 ± 0.589133
Precession(°): -149.9080 ± 76.0809

  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.