Trajectory SP806

Force field: martini_v2.2
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: 19192
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P193 AP03941
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LSALWGVAKSLF
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 9
  Polar: 2
Electrostatic Dipolar Moment (e nm): 1.76
Longitudinal (e nm): 1.66
Transversal (e nm): 0.6
Hydrophobic Dipolar Moment (nm): 1.07
Longitudinal (nm): 0.4
Transversal (nm): 0.99
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
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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): 0.642790000 ± 0.000923616
Upper leaflet (nm2): 0.642790000 ± 0.000923616
Lower leaflet (nm2): 0.642790000 ± 0.000923616
Average Z coordinate
Peptide (nm): 5.2010800 ± 0.0351744
First Residue (nm): 5.2462500 ± 0.0421593
Last Residue (nm): 5.1229300 ± 0.0411072
Membrane (nm): 6.83496000 ± 0.00999348
Upper leaflet Head Group (nm): 8.7962500 ± 0.0118277
Lower leaflet Head Group (nm): 4.8717200 ± 0.0081224
Bilayer Thickness (nm): 3.9245300 ± 0.0143481
Peptide insertion (nm): -0.32936 ± 0.03610
Contacts
Peptide - Water: 14.822500 ± 0.545014
Peptide - Head groups: 9.435000 ± 0.286968
Peptide - Tail groups: 9.780000 ± 0.224815
Tilt (°): 87.1775 ± 1.4626
PepDF:
5(ns):  CVS
Displacement (nm): 0.7894520 ± 0.0316076
Precession(°): -0.293026 ± 2.786790
50(ns)  CVS
Displacement (nm): 2.244740 ± 0.101704
Precession(°): 0.294244 ± 10.052100
100(ns)  CVS
Displacement(nm): 3.402050 ± 0.132049
Precession(°): 7.01724 ± 13.85630
200(ns)  CVS
Displacement(nm): 5.364870 ± 0.236513
Precession(°): 1.7310 ± 16.8833

  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.