Trajectory SP1235
Force field:
martini_v3
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: 17402
Time step (fs) : 25
Software: GROMACS 2021.5
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: 17402
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer:
Finisterrae III CESGA
Peptides: P406 AP01016
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W
Peptides: P406 AP01016
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W
Sequence :
FFGKMKEYFKKFGASFKRRFANLKKRL
Total charge (e): +9
Number of residues: 27
By amino acid: Basic: 10 Acidic: 1 Hydrophobic: 13 Polar: 3 Electrostatic Dipolar Moment (e nm): 2.15
Longitudinal (e nm): 1.59 Transversal (e nm): 1.45 Hydrophobic Dipolar Moment (nm): 7.02
Longitudinal (nm): 6.61 Transversal (nm): 2.36 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: POPG:POPE (1:3) (Gram-negative bacteria)
POPE
1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Total charge (e): 0
See POPE lipid
Download ITP File. Download PDB File.
POPG
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Total charge (e): -1
See POPG lipid
Download ITP File. Download PDB File.
Last snapshot
Total contacts per residue
Number of total contacts per residue type:
Number of contacts between each residue of the peptide backbone and the different lipid types, averaged over the last microsecond and using a cut-off of 0.6 nm.
Contacts per residue
(normalized by total number of beads of the amino acid):
Number of contacts between each residue of the peptide backbone and the different lipid types, averaged over the last microsecond and using a cut-off of 0.6 nm.
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): 0.61528500 ± 0.00124188
Upper leaflet (nm2): 0.61528500 ± 0.00124188
Lower leaflet (nm2): 0.61528500 ± 0.00124188
Average Z coordinate
Peptide (nm): 8.5846800 ± 0.0392229
First Residue (nm): 8.4150500 ± 0.0517412
Last Residue (nm): 8.6405100 ± 0.0503734
Membrane (nm): 6.3855200 ± 0.0124978
Upper leaflet Head Group (nm): 8.3965700 ± 0.0145787
Lower leaflet Head Group (nm): 4.3751000 ± 0.0109783
Bilayer Thickness (nm): 4.02147 ± 0.01825
Peptide insertion (nm): 0.1881170 ± 0.0418446
Contacts
Peptide - Water: 60.20000 ± 1.33133
Peptide - Head groups: 15.947500 ± 0.352254
Peptide - Tail groups: 14.352500 ± 0.287983
Tilt (°): 86.469900 ± 0.940812
Membrane (nm2): 0.61528500 ± 0.00124188
Upper leaflet (nm2): 0.61528500 ± 0.00124188
Lower leaflet (nm2): 0.61528500 ± 0.00124188
Average Z coordinate
Peptide (nm): 8.5846800 ± 0.0392229
First Residue (nm): 8.4150500 ± 0.0517412
Last Residue (nm): 8.6405100 ± 0.0503734
Membrane (nm): 6.3855200 ± 0.0124978
Upper leaflet Head Group (nm): 8.3965700 ± 0.0145787
Lower leaflet Head Group (nm): 4.3751000 ± 0.0109783
Bilayer Thickness (nm): 4.02147 ± 0.01825
Peptide insertion (nm): 0.1881170 ± 0.0418446
Contacts
Peptide - Water: 60.20000 ± 1.33133
Peptide - Head groups: 15.947500 ± 0.352254
Peptide - Tail groups: 14.352500 ± 0.287983
Tilt (°): 86.469900 ± 0.940812
PepDF:
5(ns): CVS
Displacement (nm): 0.6480680 ± 0.0258264
Precession(°): 0.333925 ± 1.337820
50(ns) CVS
Displacement (nm): 1.7483800 ± 0.0727129
Precession(°): 4.54478 ± 4.65400
100(ns) CVS
Displacement(nm): 2.425390 ± 0.106736
Precession(°): 12.84580 ± 6.25554
200(ns) CVS
Displacement(nm): 2.915420 ± 0.132714
Precession(°): 33.58570 ± 9.30269
Download JSON File.
5(ns): CVS
Displacement (nm): 0.6480680 ± 0.0258264
Precession(°): 0.333925 ± 1.337820
50(ns) CVS
Displacement (nm): 1.7483800 ± 0.0727129
Precession(°): 4.54478 ± 4.65400
100(ns) CVS
Displacement(nm): 2.425390 ± 0.106736
Precession(°): 12.84580 ± 6.25554
200(ns) CVS
Displacement(nm): 2.915420 ± 0.132714
Precession(°): 33.58570 ± 9.30269
Download JSON File.
Peptide Analyses
Peptide Displacement Fingerprint
(PepDF)
Lateral displacement vs
Rotational
Displacement along the trajectory, for different time
windows .
Tilt angle: 
Peptide tilt angle evolution, defined as the angle between the peptide helical axis and the bilayer normal .
Peptide spin: 
Evolution of the angle formed by the transversal component of the hydrophobic dipolar moment and a vector transversal to the peptide pointing outwards the membrane.
Lipid Analyses:
Area per lipid
In this system both leaflets have the same number of lipids, thus the values for their APL are overlaping in the plot
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.