Trajectory SP1365
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: 17403
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: 17403
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer:
Finisterrae III CESGA
Peptides: P471 AP04628
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W
Peptides: P471 AP04628
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W
Sequence :
RRLSKVLGKLRDKIATWRQRLLTK
Total charge (e): +8
Number of residues: 24
By amino acid: Basic: 9 Acidic: 1 Hydrophobic: 10 Polar: 4 Electrostatic Dipolar Moment (e nm): 8
Longitudinal (e nm): 7.96 Transversal (e nm): 0.79 Hydrophobic Dipolar Moment (nm): 3.59
Longitudinal (nm): 3.19 Transversal (nm): 1.66 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): 0.614428000 ± 0.000982263
Upper leaflet (nm2): 0.614428000 ± 0.000982263
Lower leaflet (nm2): 0.614428000 ± 0.000982263
Average Z coordinate
Peptide (nm): 8.6216500 ± 0.0405572
First Residue (nm): 8.6751300 ± 0.0572848
Last Residue (nm): 8.8630600 ± 0.0626174
Membrane (nm): 6.3993300 ± 0.0100717
Upper leaflet Head Group (nm): 8.4118100 ± 0.0121057
Lower leaflet Head Group (nm): 4.38685000 ± 0.00820039
Bilayer Thickness (nm): 4.0249600 ± 0.0146217
Peptide insertion (nm): 0.2098410 ± 0.0423253
Contacts
Peptide - Water: 53.8225 ± 1.1206
Peptide - Head groups: 15.175000 ± 0.338805
Peptide - Tail groups: 11.792500 ± 0.266056
Tilt (°): 84.4329 ± 1.3888
Membrane (nm2): 0.614428000 ± 0.000982263
Upper leaflet (nm2): 0.614428000 ± 0.000982263
Lower leaflet (nm2): 0.614428000 ± 0.000982263
Average Z coordinate
Peptide (nm): 8.6216500 ± 0.0405572
First Residue (nm): 8.6751300 ± 0.0572848
Last Residue (nm): 8.8630600 ± 0.0626174
Membrane (nm): 6.3993300 ± 0.0100717
Upper leaflet Head Group (nm): 8.4118100 ± 0.0121057
Lower leaflet Head Group (nm): 4.38685000 ± 0.00820039
Bilayer Thickness (nm): 4.0249600 ± 0.0146217
Peptide insertion (nm): 0.2098410 ± 0.0423253
Contacts
Peptide - Water: 53.8225 ± 1.1206
Peptide - Head groups: 15.175000 ± 0.338805
Peptide - Tail groups: 11.792500 ± 0.266056
Tilt (°): 84.4329 ± 1.3888
PepDF:
5(ns): CVS
Displacement (nm): 0.6452640 ± 0.0264275
Precession(°): 0.0898275 ± 1.4864000
50(ns) CVS
Displacement (nm): 1.7208200 ± 0.0822219
Precession(°): -0.147926 ± 3.497940
100(ns) CVS
Displacement(nm): 2.181990 ± 0.121929
Precession(°): 1.56843 ± 4.44899
200(ns) CVS
Displacement(nm): 3.017210 ± 0.170769
Precession(°): 11.4101 ± 5.7821
Download JSON File.
5(ns): CVS
Displacement (nm): 0.6452640 ± 0.0264275
Precession(°): 0.0898275 ± 1.4864000
50(ns) CVS
Displacement (nm): 1.7208200 ± 0.0822219
Precession(°): -0.147926 ± 3.497940
100(ns) CVS
Displacement(nm): 2.181990 ± 0.121929
Precession(°): 1.56843 ± 4.44899
200(ns) CVS
Displacement(nm): 3.017210 ± 0.170769
Precession(°): 11.4101 ± 5.7821
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.