Lipid Height Calculations

The HeightPlotter code calculates the average height of lipids (Phosphate or C2 to midplane distance) and the bilayer thickness. The output contains three figures: one for the builayer thickness, one for the upper leaflet height, and one for the lower leflet height. The lipids heights are averages over a specified block of simualtion time (trjst to trjsp). If this time is too short, then area on the plots will have a height of zero. If blocks are too short, then peptides may blur as averages flatten.


Minimum Requirements

Calculations require:


Two-component bilayer (for 1 component system, set both LipidA and LipidB to same peptide. Trajectory name is dyn$N.trj, where $N is a number between TrjSt and TrjSp or, if ‘path’ ends with ‘.trj’ or ‘.dcd’, read only that file.

Peptides are colored as gray, purple (Charged), and white (Histidine) circles. This should be easy to modify in furture versions.

Optional Keywords for the Input File

Keyword Values
Title Title on figures
PSF Location of psf
path Path for trajectory files
LipidA Residue name for lipid A
LipidB Residue name for lipid B (use same as Lipid B no Lipid A)
trjst Number of first trajectory file
trjsp Number of last trajectory file
out Output file name
Translate If True, translate each frame so N-termini are at center
Rotate If True, rotate each frame so N-termmini is at the 6 o’clock Position and the C-termini is at the 12 o’clock position. This is best Used when ‘Translate’ is also True
pbcsym Symmetry of unit cell, P1 or P21 only
phosphates If True, use phosphates to determine lipid height. If False, use C2 of sn-2 chain.
plottype ColorMap, Contour, or Voronoi. Voronoi currenty not working.
EmptyCell If cell has zero population, ‘Zero’ keeps a zero value and ‘Neighbors’ Fills the cell with an average of neighboring cells. If all neighboring Cells are empty, the program will crash!
ShowNeighbors If True, show image peptides. If False, don’t.
IncludeHist If True, include histograms of tilt, depths of insertion, and rotation. All three properties must be calculated beforehand.

Example Input File:

Title         p1 3:1 PC/PG P21
PSF           /u/bsp6/Proj/piscidin/DMPC_DMPG_FEP1/SetupPcPgP1_FREE/pcpgp1_p21_mini_free.psf
path          /u/bsp6/Proj/piscidin/DMPC_DMPG_FEP1/DynPcPgP1_FREE/
LipidA        DMPC
LipidB        DMPG
trjst         43
trjsp         62
out           run43-62_skip20
Translate     True
Rotate        True
pbcsym        P21
phosphates    False
plottype      ColorMap
EmptyCell     Neighbors
ShowNeighbors False
IncludeHist   True

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