Trajectory SP1348

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: 19200
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P463 AP03759
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
RLKRLRKKLKKLLKKLS
Total charge (e): +10
Number of residues: 17
By amino acid:
  Basic: 10
  Acidic: 0
  Hydrophobic: 6
  Polar: 1
Electrostatic Dipolar Moment (e nm): 6.84
Longitudinal (e nm): 6.49
Transversal (e nm): 2.17
Hydrophobic Dipolar Moment (nm): 3.36
Longitudinal (nm): 2.56
Transversal (nm): 2.17
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
 
  Download PDB File.
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): 0.64784300 ± 0.00130801
Upper leaflet (nm2): 0.64784300 ± 0.00130801
Lower leaflet (nm2): 0.64784300 ± 0.00130801
Average Z coordinate
Peptide (nm): 7.21743 ± 2.06786
First Residue (nm): 7.14177 ± 2.11794
Last Residue (nm): 7.29195 ± 2.02214
Membrane (nm): 6.8355000 ± 0.0136424
Upper leaflet Head Group (nm): 8.7796600 ± 0.0162327
Lower leaflet Head Group (nm): 4.8921200 ± 0.0110061
Bilayer Thickness (nm): 3.8875500 ± 0.0196122
Peptide insertion (nm): -1.56223 ± 2.06792
Contacts
Peptide - Water: 89.052500 ± 0.657643
Peptide - Head groups: 0.205000 ± 0.154088
Peptide - Tail groups: 0.00250000 ± 0.00845298
Tilt (°): 96.50000 ± 8.57717
PepDF:
5(ns):  CVS
Displacement (nm): 1.8173900 ± 0.0783781
Precession(°): 8.86103 ± 13.54620
50(ns)  CVS
Displacement (nm): 5.514870 ± 0.303516
Precession(°): 106.9700 ± 40.6667
100(ns)  CVS
Displacement(nm): 7.743160 ± 0.504097
Precession(°): 243.8970 ± 53.4486
200(ns)  CVS
Displacement(nm): 10.831100 ± 0.877908
Precession(°): 483.0220 ± 71.3251

  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.