Trajectory SP890

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: 19195
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P235 NC02940
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
ANTPCGPYTHDCPVKR
Total charge (e): +1
Number of residues: 16
By amino acid:
  Basic: 5
  Acidic: 1
  Hydrophobic: 6
  Polar: 6
Electrostatic Dipolar Moment (e nm): 1.5
Longitudinal (e nm): 1.16
Transversal (e nm): 0.96
Hydrophobic Dipolar Moment (nm): 1.59
Longitudinal (nm): 1.59
Transversal (nm): 0.01
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): 0.64280500 ± 0.00121169
Upper leaflet (nm2): 0.64280500 ± 0.00121169
Lower leaflet (nm2): 0.64280500 ± 0.00121169
Average Z coordinate
Peptide (nm): 9.0226500 ± 0.0415418
First Residue (nm): 8.7492600 ± 0.0443365
Last Residue (nm): 9.1842100 ± 0.0866811
Membrane (nm): 6.8333100 ± 0.0127011
Upper leaflet Head Group (nm): 8.792790 ± 0.015212
Lower leaflet Head Group (nm): 4.8743900 ± 0.0105174
Bilayer Thickness (nm): 3.9184000 ± 0.0184939
Peptide insertion (nm): 0.2298550 ± 0.0442394
Contacts
Peptide - Water: 32.02000 ± 1.14819
Peptide - Head groups: 10.550000 ± 0.294527
Peptide - Tail groups: 6.407500 ± 0.316513
Tilt (°): 78.95170 ± 2.59955
PepDF:
5(ns):  CVS
Displacement (nm): 0.7364760 ± 0.0322996
Precession(°): -0.790859 ± 2.671270
50(ns)  CVS
Displacement (nm): 2.0567800 ± 0.0885672
Precession(°): -4.25466 ± 10.19880
100(ns)  CVS
Displacement(nm): 2.760110 ± 0.125598
Precession(°): 1.81418 ± 15.72320
200(ns)  CVS
Displacement(nm): 4.326610 ± 0.196419
Precession(°): -5.19845 ± 26.74970

  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.