Trajectory SP1111

Force field: martini_v2.2P
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: 45483
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P345 NC00592
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
FAKKLAKLAKKALAL
Total charge (e): +5
Number of residues: 15
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 10
  Polar: 0
Electrostatic Dipolar Moment (e nm): 3.94
Longitudinal (e nm): 3.59
Transversal (e nm): 1.64
Hydrophobic Dipolar Moment (nm): 1.84
Longitudinal (nm): 1.29
Transversal (nm): 1.31
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): 0.64897900 ± 0.00113112
Upper leaflet (nm2): 0.64897900 ± 0.00113112
Lower leaflet (nm2): 0.64897900 ± 0.00113112
Average Z coordinate
Peptide (nm): 4.6820600 ± 0.0404392
First Residue (nm): 4.7560700 ± 0.0426622
Last Residue (nm): 4.8328200 ± 0.0539536
Membrane (nm): 6.5744000 ± 0.0111901
Upper leaflet Head Group (nm): 8.5423500 ± 0.0127826
Lower leaflet Head Group (nm): 4.60464000 ± 0.00927219
Bilayer Thickness (nm): 3.9377100 ± 0.0157914
Peptide insertion (nm): -0.0774244 ± 0.0414886
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 10.097500 ± 0.239145
Peptide - Tail groups: 10.130000 ± 0.249621
Tilt (°): 95.33750 ± 1.42076
PepDF:
5(ns):  CVS
Displacement (nm): 0.7010430 ± 0.0304683
Precession(°): -0.0360048 ± 1.7365600
50(ns)  CVS
Displacement (nm): 2.55766 ± 0.12909
Precession(°): 1.10528 ± 5.91891
100(ns)  CVS
Displacement(nm): 3.931880 ± 0.183145
Precession(°): 7.70658 ± 8.82367
200(ns)  CVS
Displacement(nm): 5.336700 ± 0.315804
Precession(°): 23.2748 ± 9.2400

  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.