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METHODS
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METHODS
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#==========================================================================================================================
# METHODS ### These scripts and processes were developed over a two year period in support of my doctoral research.
# ### Their development was an evolutionary process. None of this work was imagined or planned in the beginning.
# ### Unexpected results were encountered, and processes were developed to better measure and verify the initial
# ### indications. This process is nowhere close to being complete. There is much more work to do to better
# ### understand what has been discovered, and to bring more utility to the work that has been completed so far.
# ###
# ### It is beyond the scope of this document to explain everything that is taking place. The purpose of this
# ### document is to outline the sequence of steps required to implement these tools on simulation trajectories
# ### to produce the resulting analysis. At some point, I hope to provide a single master script and simulation
# ### setup that adopters could run on their systems to get a complete "under the hood" look at all the
# ### mechanics.
# ###
# ### The first step to understanding this work would be to read my paper, Insights into the molecular
# ### mechanisms of electroporation from computational elecrophysiology, in Biophysical Journal, especially the
# ### supporting information. This will give an introduction of the scripts select. and shift. These enable a
# ### very accurate count of water molecules in a membrane pore on a frame by frame basis. They also prepare the
# ### trajectories for the following processing.
# ###
# ### The title of my dissertation proposal was "Mapping three-dimensional interactions between biomolecules and
# ### electric fields". To do this, I needed to create trajectories that had all extraneous motion relative to
# ### the biostructure I wanted to study the effect of the non-linear electric fields on, and have that
# ### biostructure perfectly centered in the middle of the simulation box. While I was checking the raw data
# ### files at the end of those steps to verify the integrity of that processing, I created an image I had never
# ### imagined creating. We have dubbed these images "Computational X-Rays". There is lots of work yet to fully
# ### develop the cababilities of the technique, however we have produced an image that should fully demonstrate
# ### the nature of what will come of that work.
# ###
# ### I think the best way to approach this is to show the sequence of commands to produce the final images to
# ### be generated. I'll intersperse comments as needed.
# ###
# ### These steps run the initial simulation, then do a quick (cheap computationally) analysis to create some
# ### plots that can be reviewed to make sure everything looks OK.
# gmx mdrun -cpi
# gmx trjconv -f traj_comp.xtc -o trajout.xtc -pbc mol -skip 10 < <(echo -e "System\n")
# gmx select -f trajout.xtc -n index.ndx -s topol.tpr -os waters.xvg -select 'dyn_mol_com of resname TIP3
# and ((z+.75) > (z of com of (group DOPC and name P)) and (z-.75) < (z of com of (group DOPC and name P)))'
# gmx select -f trajout.xtc -n index.ndx -s topol.tpr -os watersb.xvg -select 'dyn_mol_com of resname TIP3
# and ((z+.75) > (z of com of (group D2PC and name P)) and (z-.75) < (z of com of (group D2PC and name P)))'
# source ../jobs/cross.
# gnuplot -c ../jobs/cross
# ###
# ### The next steps make very accurate counts of membrane pore water molecules.
# source ../jobs/select. twatc
# source ../jobs/select. bwatc
# source ../jobs/shift. run
# source ../jobs/count.
# ###
# ### Now for each membrane pore (each of two membranes in the sim have one pore), a trajectory is produced
# ### in which the center of the pore is translated to the exact center of the simulation box. From these
# ### trajectories, a set of coordinates for every atom in every frame of the simulation is created (coord.xvg).
# ### This file is used by script 3dchrg4A.awk to produce the composite electric charge map of the simulation
# ### volume elements. Finally, this file is processed by Bfintegr8.awk to produce the electric field and
# ### potential maps. In this example, channel 0 (top) is being processed. #!NOTE: Since my work has focused at
# ### this point on the analysis of only one of the two pores in any single simulation, the file names would
# ### conflict if both pores were analyzed simultaneously.
# source ../jobs/center. 0
# gmx trajectory -f trajout0c.xtc -ox coord.xvg -n index.ndx < <(echo -e 'System\n')
# source ../jobs/3dchrg4A.awk 50 chrgs3.xvg chrg5A.xvg
# source ../jobs/3dchrg4H.awk 50 chrgs3.xvg chrg5H.xvg 1 4 10 11
# source ../jobs/3dchrg4N.awk 50 chrgs3.xvg chrg5N.xvg 1 4 10 11
# source ../jobs/3dchrg4C.awk 50 chrgs3.xvg chrg5C.xvg 1 4 10 11
# source ../jobs/3dchrg4P.awk 50 chrgs3.xvg chrg5P.xvg 1 4 10 11
# source ../jobs/3dchrg4W.awk 50 chrgs3.xvg chrg5W.xvg 1 4 10 11
# source ../jobs/3dchrg4R.awk 50 chrgs3.xvg chrg5R.xvg 1 4 10 11
# source ../jobs/3dchrg4T.awk 50 chrgs3.xvg chrg5T.xvg 1 4 10 11
# source ../jobs/3dchrg4Y.awk 50 chrgs3.xvg chrg5Y.xvg 1 4 10 11
# source ../jobs/3dchrg4L.awk 50 chrgs3.xvg chrg5L.xvg 1 4 10 11
# source ../jobs/3dchrg4S.awk 50 chrgs3.xvg chrg5S.xvg 1 4 10 11
# #!NOTE The above 11 lines can be invoked with source lchrgall.
# source ../jobs/Bfintegr8.awk 50 chrg5A.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5H.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5N.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5C.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5P.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5W.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5R.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5T.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5Y.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5L.xvg
# source ../jobs/Bfintegr8.awk 50 chrg5S.xvg
# for s in A H N P W S C R T L Y; do
# s ../jobs/spltfld. ${ARG2:0:1} ${s}
# done
# #!NOTE The above 11 invocations of Bfintegr8.awk can be invoked with source integr8all.
# gnuplot -c plfldmaps
# ###
# ### The Net Electric Flux maps show the resulting field and potential for every atom in the system. The
# ### The plot with the fyld* name shows the electric field and the plot with the fylt* name shows the
# ### potential. The other plots show the same fields and potentials for the indicated moieties in the system.
# ### Some of these are in the range of ten times the magnitude of the overall field and potential. Each plot
# ### is scaled to reveal all the detail present in the maps for that particular moiety. The relative values of
# ### these scales are contained in the a[subscript] array in the gnuplot script plfldmaps.
# ###
# ### I have also uploaded some of the first images to come out of the computational x-ray work, but will delay
# ### providing the coding and procedures pending the publication of the first paper on the subject.
#_________________________________________________________________________________________________________________________