Trajectory SP1444

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: 19211
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P511 NC03115
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
GCCSFAACRKYRPEMCG
Total charge (e): +2
Number of residues: 17
By amino acid:
  Basic: 3
  Acidic: 1
  Hydrophobic: 7
  Polar: 6
Electrostatic Dipolar Moment (e nm): 3.88
Longitudinal (e nm): 3.6
Transversal (e nm): 1.45
Hydrophobic Dipolar Moment (nm): 2.38
Longitudinal (nm): 2.37
Transversal (nm): 0.3
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): 0.64895300 ± 0.00112297
Upper leaflet (nm2): 0.64895300 ± 0.00112297
Lower leaflet (nm2): 0.64895300 ± 0.00112297
Average Z coordinate
Peptide (nm): 5.11392 ± 1.35507
First Residue (nm): 5.22895 ± 1.24541
Last Residue (nm): 4.93379 ± 1.48978
Membrane (nm): 6.8325000 ± 0.0113147
Upper leaflet Head Group (nm): 8.7740200 ± 0.0135884
Lower leaflet Head Group (nm): 4.89150000 ± 0.00939143
Bilayer Thickness (nm): 3.882530 ± 0.016518
Peptide insertion (nm): -0.222421 ± 1.355100
Contacts
Peptide - Water: 49.71000 ± 5.56206
Peptide - Head groups: 7.15250 ± 1.79928
Peptide - Tail groups: 3.71500 ± 1.21705
Tilt (°): 78.95010 ± 5.05591
PepDF:
5(ns):  CVS
Displacement (nm): 1.1445300 ± 0.0657111
Precession(°): 3.58095 ± 9.62370
50(ns)  CVS
Displacement (nm): 3.537300 ± 0.264969
Precession(°): 35.3196 ± 34.9581
100(ns)  CVS
Displacement(nm): 4.650920 ± 0.332767
Precession(°): 74.1030 ± 50.3512
200(ns)  CVS
Displacement(nm): 7.426720 ± 0.479848
Precession(°): 274.1540 ± 58.9419

  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.