Add some trajectory analysis scripts
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cryobry
175
trajectory_analysis/6-energy.sh
Executable file
175
trajectory_analysis/6-energy.sh
Executable file
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#!/usr/bin/env bash
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export VMDNOCUDA=1
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#export VMDNOOPTIX=1
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export VMDNOOSPRAY=1
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#######################################################################################
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## ADJUSTABLE PARAMETERS ##
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#######################################################################################
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# set step size for dcd file incrementing
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step_size=10000000
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# set folder name that contains the jobs
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job_folder="4-new_jobs"
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# set sel1
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sel1="chain B and not resname PHQ"
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# set sel2
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sel2="chain A"
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# only run specific systems
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my_systems=("ALL")
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#######################################################################################
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## FUNCTIONS ##
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#######################################################################################
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function get_systems() {
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systems=()
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all_systems=()
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_jobs=( $(ls -d ../${job_folder}/*/*/) )
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for _job in ${_jobs[@]}; do
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all_systems+=( $(basename ${_job}) )
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done
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systems+=( $(for _system in ${all_systems[@]}; do echo ${_system}; done | sort -u) )
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}
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function get_ffs() {
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ffs=()
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for ff in ../0-forcefields/*; do
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if [[ -f "${ff}" ]]; then
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ffs+=(${ff})
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fi
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done
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}
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#######################################################################################
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## ENERGY ANALYSIS ##
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#######################################################################################
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# set folder name for output files
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out_dir="$(basename ${0})"
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out_dir="${out_dir%%.*}2"
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function namd_energy() {
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get_systems
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get_ffs
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mkdir -p ${out_dir}
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ffs_energy=""
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for ff in ${ffs[@]}; do
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ffs_energy+="-par \"${ff}\" "
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done
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for system in "${systems[@]}"; do
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if echo ${my_systems[@]} | grep -w ${system} > /dev/null; then
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jobs=( $(ls -d ../${job_folder}/*/${system}/) )
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for job in ${jobs[@]}; do
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job=${job%%/}
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date=${job#*/*/}
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date=${date%/*}
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dcds=( $(ls ${job}/*sim_*.dcd | sort -V) )
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xscs=( $(ls ${job}/*sim_*.xsc | sort -V) )
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# Run NAMDEnergy
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echo 'package require namdenergy' > temp.tcl
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echo "set sel1 [atomselect top \"${sel1}\"]" >> temp.tcl
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echo "set sel2 [atomselect top \"${sel2}\"]" >> temp.tcl
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echo "namdenergy -vdw -elec -nonb -sel \$sel1 \$sel2 -ofile \""${out_dir}/${system}-${date}.csv"\" -tempname \""${system}-${date}"\" -switch 10 -cutoff 12 -diel 1.0 -T 310 -timemult 2 -stride 10000 -extsys "${xscs[0]}" -pme ${ffs_energy} -exe "/home/bryan/bin/namd2" -plot" >> temp.tcl
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echo 'exit' >> temp.tcl
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# run temp.tcl
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vmd -dispdev text -eofexit ${job}/${system}_solv_ion.psf ${dcds[@]:1} < "temp.tcl"
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rm "temp.tcl"
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done
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awk 'FNR == 1 { nfiles++; ncols = NF }
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{ for (i = 1; i < NF; i++) sum[FNR,i] += $i
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if (FNR > maxnr) maxnr = FNR
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}
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END {
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for (line = 1; line <= maxnr; line++)
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{
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for (col = 1; col < ncols; col++)
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printf " %.2f", sum[line,col]/nfiles;
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printf "\n"
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}
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}' ${out_dir}/${system}-* > ${out_dir}/${system}-combined.csv
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fi
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rm FFTW_NAMD*
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plot_energy ${system} ${out_dir}/${system}-combined
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done
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}
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function plot_energy() {
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gnuplot -persist <<-GNUPLOT_INPUT
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set terminal pngcairo enhanced size 1600,1200 font "arial,24" linewidth 2
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set output "${2}.png"
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set autoscale
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set title "SrtA-{/Arial-Italic Boc} interaction energy" font "arial,40"
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set xlabel "Time (ns)" font "arial,32"
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set ylabel "Energy (kcal/mol)" font "arial,32"
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set border 1+2
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#set xtics nomirror
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set ytics nomirror
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set grid
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set grid noxtics
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set key box off
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set yrange [-25:0]
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#set format y "%+-2.f"
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set style data lines
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set xzeroaxis ls 8
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# linetypes
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#set style line 1 pi 0 lw 1 ps 1 pt 0 lc rgb '#000000'
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plot "${2}.csv" using (\$1 / 50):5 with linespoints ls 8 pi 0 pt 0
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exit
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GNUPLOT_INPUT
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}
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function plot_energy2() {
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gnuplot -persist <<-GNUPLOT_INPUT
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set terminal pngcairo enhanced size 1600,1200 font "arial,24" linewidth 2
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set output "ALL-combined-both.png"
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set datafile separator ","
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set autoscale
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set title "SrtA-{/Arial-Italic Boc} interaction energy" font "arial,40"
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set xlabel "Time (ns)" font "arial,32"
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set ylabel "Energy (kcal/mol)" font "arial,32"
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set border 1+2
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#set xtics nomirror
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set ytics nomirror
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set grid
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set grid noxtics
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set key box right bottom
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set yrange [-80:0]
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#set format y "%+-2.f"
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set style data filledcurves
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#set xzeroaxis ls 8
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# linetypes
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set style line 1 pi 0 lw 1 ps 1 pt 0 lc rgb '#696969'
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set style line 2 pi 0 lw 1 ps 1 pt 0 lc rgb 'black'
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plot 'ALL-combined-both.csv' using (\$1 / 50):(\$3 + \$4) title 'SS peptide' with filledcurves y1=0 ls 1, \
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'' using (\$1 / 50):(\$3) title '{/Arial-Italic Boc}' with filledcurves y1=0 ls 2
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exit
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GNUPLOT_INPUT
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}
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namd_energy
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