Trajectory SP1460

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: 19217
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P519 NC03835
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
YGGFMKPYTQQSHKPLITLLKHVTLKNEQ
Total charge (e): +3
Number of residues: 29
By amino acid:
  Basic: 10
  Acidic: 1
  Hydrophobic: 12
  Polar: 10
Electrostatic Dipolar Moment (e nm): 6.26
Longitudinal (e nm): 6.24
Transversal (e nm): 0.58
Hydrophobic Dipolar Moment (nm): 5.21
Longitudinal (nm): 5.15
Transversal (nm): 0.8
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): 0.64931100 ± 0.00157013
Upper leaflet (nm2): 0.64931100 ± 0.00157013
Lower leaflet (nm2): 0.64931100 ± 0.00157013
Average Z coordinate
Peptide (nm): 4.4615500 ± 0.0694168
First Residue (nm): 4.8434700 ± 0.0429333
Last Residue (nm): 3.870870 ± 0.131982
Membrane (nm): 6.8249100 ± 0.0164271
Upper leaflet Head Group (nm): 8.7646600 ± 0.0192725
Lower leaflet Head Group (nm): 4.8859900 ± 0.0135836
Bilayer Thickness (nm): 3.8786700 ± 0.0235784
Peptide insertion (nm): 0.4244430 ± 0.0707333
Contacts
Peptide - Water: 69.4600 ± 3.6008
Peptide - Head groups: 13.96250 ± 0.82374
Peptide - Tail groups: 10.320000 ± 0.750786
Tilt (°): 79.88750 ± 2.23074
PepDF:
5(ns):  CVS
Displacement (nm): 0.7959570 ± 0.0349094
Precession(°): 0.54740 ± 1.88987
50(ns)  CVS
Displacement (nm): 2.538180 ± 0.148503
Precession(°): 7.52123 ± 6.80848
100(ns)  CVS
Displacement(nm): 3.756620 ± 0.172317
Precession(°): 19.7366 ± 7.7859
200(ns)  CVS
Displacement(nm): 5.217590 ± 0.303297
Precession(°): 39.98380 ± 7.02949

  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.