Trajectory SP874

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: 19189
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P227 NC02428
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
CCRLSCGLGCHPCC
Total charge (e): +1
Number of residues: 14
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 5
  Polar: 7
Electrostatic Dipolar Moment (e nm): 3.18
Longitudinal (e nm): 3.07
Transversal (e nm): 0.8
Hydrophobic Dipolar Moment (nm): 0.76
Longitudinal (nm): 0.72
Transversal (nm): 0.24
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): 0.64249800 ± 0.00102317
Upper leaflet (nm2): 0.64249800 ± 0.00102317
Lower leaflet (nm2): 0.64249800 ± 0.00102317
Average Z coordinate
Peptide (nm): 5.047480 ± 0.040402
First Residue (nm): 5.076340 ± 0.043878
Last Residue (nm): 4.9769600 ± 0.0460611
Membrane (nm): 6.8352000 ± 0.0108801
Upper leaflet Head Group (nm): 8.7957500 ± 0.0130542
Lower leaflet Head Group (nm): 4.87277000 ± 0.00880853
Bilayer Thickness (nm): 3.9229800 ± 0.0157481
Peptide insertion (nm): -0.1747140 ± 0.0413511
Contacts
Peptide - Water: 19.215000 ± 0.681351
Peptide - Head groups: 10.525000 ± 0.261109
Peptide - Tail groups: 9.225000 ± 0.270976
Tilt (°): 92.51060 ± 1.26817
PepDF:
5(ns):  CVS
Displacement (nm): 0.7470920 ± 0.0319511
Precession(°): -2.61211 ± 2.55740
50(ns)  CVS
Displacement (nm): 2.2936900 ± 0.0975498
Precession(°): -25.99170 ± 7.67204
100(ns)  CVS
Displacement(nm): 2.714820 ± 0.136068
Precession(°): -47.0957 ± 11.3106
200(ns)  CVS
Displacement(nm): 3.384530 ± 0.181248
Precession(°): -93.3037 ± 13.2550

  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.