Trajectory SP700

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: 19196
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P140 AP01545
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
FGHLFKLATKIIPSLFQ
Total charge (e): +2
Number of residues: 17
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 11
  Polar: 3
Electrostatic Dipolar Moment (e nm): 3.38
Longitudinal (e nm): 3.14
Transversal (e nm): 1.25
Hydrophobic Dipolar Moment (nm): 1.48
Longitudinal (nm): 0.1
Transversal (nm): 1.47
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)
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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): 0.64375500 ± 0.00102771
Upper leaflet (nm2): 0.64375500 ± 0.00102771
Lower leaflet (nm2): 0.64375500 ± 0.00102771
Average Z coordinate
Peptide (nm): 8.549650 ± 0.035802
First Residue (nm): 8.5504200 ± 0.0410805
Last Residue (nm): 8.8066500 ± 0.0414198
Membrane (nm): 6.8208600 ± 0.0105495
Upper leaflet Head Group (nm): 8.7823700 ± 0.0125256
Lower leaflet Head Group (nm): 4.86252000 ± 0.00875077
Bilayer Thickness (nm): 3.9198500 ± 0.0152796
Peptide insertion (nm): -0.2327250 ± 0.0379299
Contacts
Peptide - Water: 22.120000 ± 0.597978
Peptide - Head groups: 12.102500 ± 0.235561
Peptide - Tail groups: 12.12500 ± 0.29589
Tilt (°): 88.75880 ± 1.02296
PepDF:
5(ns):  CVS
Displacement (nm): 0.6676420 ± 0.0266678
Precession(°): -0.142488 ± 2.057500
50(ns)  CVS
Displacement (nm): 1.792010 ± 0.101266
Precession(°): -2.39953 ± 6.55143
100(ns)  CVS
Displacement(nm): 2.267470 ± 0.108386
Precession(°): -2.19058 ± 8.88205
200(ns)  CVS
Displacement(nm): 3.209570 ± 0.140889
Precession(°): -0.518373 ± 14.494900

  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.