Trajectory SP1177

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: 45460
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P378 NC03629
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
MRKWFHNVLSSGQLLADKWPAWDYNRK
Total charge (e): +3
Number of residues: 27
By amino acid:
  Basic: 8
  Acidic: 2
  Hydrophobic: 13
  Polar: 6
Electrostatic Dipolar Moment (e nm): 6.34
Longitudinal (e nm): 6.32
Transversal (e nm): 0.57
Hydrophobic Dipolar Moment (nm): 6.81
Longitudinal (nm): 6.71
Transversal (nm): 1.18
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): 0.649740000 ± 0.000850652
Upper leaflet (nm2): 0.649740000 ± 0.000850652
Lower leaflet (nm2): 0.649740000 ± 0.000850652
Average Z coordinate
Peptide (nm): 8.6647100 ± 0.0373591
First Residue (nm): 8.4553500 ± 0.0443002
Last Residue (nm): 8.94954 ± 0.07256
Membrane (nm): 6.5658900 ± 0.0083426
Upper leaflet Head Group (nm): 8.5318700 ± 0.0101016
Lower leaflet Head Group (nm): 4.60036000 ± 0.00676991
Bilayer Thickness (nm): 3.9315200 ± 0.0121604
Peptide insertion (nm): 0.1328400 ± 0.0387007
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 16.255000 ± 0.337966
Peptide - Tail groups: 13.890000 ± 0.431437
Tilt (°): 83.62410 ± 1.22758
PepDF:
5(ns):  CVS
Displacement (nm): 0.5786280 ± 0.0235502
Precession(°): 0.665506 ± 1.015480
50(ns)  CVS
Displacement (nm): 1.7087100 ± 0.0826782
Precession(°): 7.29683 ± 2.53047
100(ns)  CVS
Displacement(nm): 2.204460 ± 0.123004
Precession(°): 15.47020 ± 3.95909
200(ns)  CVS
Displacement(nm): 2.23460 ± 0.12926
Precession(°): 23.45950 ± 6.11163

  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.