Trajectory SP1252

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: 19208
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P415 AP01623
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
FKLKGMARISCLPNGQWSNFPPKCIRECAMVSS
Total charge (e): +4
Number of residues: 33
By amino acid:
  Basic: 5
  Acidic: 1
  Hydrophobic: 17
  Polar: 10
Electrostatic Dipolar Moment (e nm): 11.72
Longitudinal (e nm): 11.53
Transversal (e nm): 2.08
Hydrophobic Dipolar Moment (nm): 1.45
Longitudinal (nm): 0.27
Transversal (nm): 1.42
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)
  Download PDB File.

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): 0.64952400 ± 0.00108164
Upper leaflet (nm2): 0.64952400 ± 0.00108164
Lower leaflet (nm2): 0.64952400 ± 0.00108164
Average Z coordinate
Peptide (nm): 9.1106100 ± 0.0565445
First Residue (nm): 8.8416000 ± 0.0560028
Last Residue (nm): 9.642340 ± 0.120872
Membrane (nm): 6.8181700 ± 0.0114159
Upper leaflet Head Group (nm): 8.7561300 ± 0.0136971
Lower leaflet Head Group (nm): 4.87847000 ± 0.00914151
Bilayer Thickness (nm): 3.8776600 ± 0.0164674
Peptide insertion (nm): 0.3544840 ± 0.0581798
Contacts
Peptide - Water: 72.20750 ± 1.85662
Peptide - Head groups: 16.022500 ± 0.438361
Peptide - Tail groups: 12.215000 ± 0.485116
Tilt (°): 81.91800 ± 1.25176
PepDF:
5(ns):  CVS
Displacement (nm): 0.7580250 ± 0.0336878
Precession(°): -0.204777 ± 1.593670
50(ns)  CVS
Displacement (nm): 2.570930 ± 0.125912
Precession(°): -1.66427 ± 5.02539
100(ns)  CVS
Displacement(nm): 3.782350 ± 0.185771
Precession(°): -6.14891 ± 6.55578
200(ns)  CVS
Displacement(nm): 5.749640 ± 0.248613
Precession(°): -13.55270 ± 7.02671

  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.