Add some trajectory analysis scripts
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cryobry
227
trajectory_analysis/1-concat.sh
Executable file
227
trajectory_analysis/1-concat.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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# number of frames to skip (i.e. from equilibration)
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skip=0
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# set folder name that contains the jobs
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job_folder="4-jobs"
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# set atom selection for concatenation
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concat_sel="chain A"
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# set atom selection to unwrap
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unwrap_sel="chain A"
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# set atom selection to wrap to
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wrap_to_sel="chain A"
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# set atom selection to wrap
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wrap_sel="chain A"
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# set atom selection for alignment
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align_sel="chain A"
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# set atom selection for EDA
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eda_sel="chain A and name CA"
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#######################################################################################
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## SET VARS ##
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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%%.*}"
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# create suffixes for output files
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concat_sel_s="${concat_sel// /_}"
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eda_sel_s="${eda_sel// /_}"
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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 ${_system}; done | sort -u) )
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}
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#######################################################################################
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## CONCATENATE, UNWRAP, ALIGN INDVIDUAL REPLICATES ##
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#######################################################################################
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function concat_individual() {
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get_systems
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for system in "${systems[@]}"; do
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dcds=()
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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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rel_job_path=${job#../${job_folder}/}
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mkdir -p ${out_dir}/individual/${rel_job_path}
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dcds=( $(ls ${job}/*sim_*.dcd | sort -V) )
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for dcd in ${dcds[@]}; do
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filename=${dcd##*/}
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filename=${filename%%.*}
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# UNWRAP AND ALIGN
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echo 'package require pbctools' > temp.tcl
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echo "pbc unwrap -all -sel \""${unwrap_sel}"\"" >> temp.tcl
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echo "pbc wrap -sel \""${wrap_sel}"\" -all -compound chain -center com -centersel \""${wrap_to_sel}"\"" >> temp.tcl
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echo "set out [atomselect top \""${concat_sel}"\"]" >> temp.tcl
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echo "animate write dcd ${out_dir}/individual/${rel_job_path}/temp-${filename}-${concat_sel_s}.dcd sel \$out waitfor all" >> temp.tcl
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for (( i=0; i<1; i++)); do
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echo "\$out writepsf ${out_dir}/individual/${rel_job_path}/${system}-${concat_sel_s}.psf" >> temp.tcl
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echo "\$out writepdb ${out_dir}/individual/${rel_job_path}/${system}-${concat_sel_s}.pdb" >> temp.tcl
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done
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echo "sync" >> 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 ${dcd} < "temp.tcl"
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sync
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rm "temp.tcl"
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done
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dcds=( $(ls ${out_dir}/individual/${rel_job_path}/temp-*-${concat_sel_s}.dcd | sort -V) )
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echo "set ref [atomselect top \""${align_sel}"\" frame 0]" > temp.tcl
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echo "set sel [atomselect top \""${align_sel}"\"]" >> temp.tcl
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echo 'set all [atomselect top "all"]' >> temp.tcl
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echo 'set n [molinfo top get numframes]' >> temp.tcl
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echo 'for { set i 1 } { $i < $n } { incr i } {' >> temp.tcl
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echo ' $sel frame $i' >> temp.tcl
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echo ' $all frame $i' >> temp.tcl
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echo ' $all move [measure fit $sel $ref]' >> temp.tcl
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echo '}' >> temp.tcl
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echo "animate write dcd ${out_dir}/individual/${rel_job_path}/${system}-${concat_sel_s}.dcd beg ${skip} waitfor all" >> temp.tcl
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echo "sync" >> 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 ${out_dir}/individual/${rel_job_path}/${system}-${concat_sel_s}.psf ${dcds[@]} < "temp.tcl"
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sync
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rm "temp.tcl"
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rm ${out_dir}/individual/${rel_job_path}/temp*
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done
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done
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}
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#######################################################################################
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## CONCATENATE AND ALIGN ALL REPLICATES ##
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#######################################################################################
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function concat_combined() {
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get_systems
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mkdir -p ${out_dir}/combined
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for system in ${systems[@]}; do
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# create dcd array and copy pdb/psf
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dcds=( $(ls ${out_dir}/individual/*/${system}/${system}-${concat_sel_s}.dcd | sort -V) )
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psfs=( $(ls ${out_dir}/individual/*/${system}/${system}-${concat_sel_s}.psf | sort -V) )
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pdbs=( $(ls ${out_dir}/individual/*/${system}/${system}-${concat_sel_s}.pdb | sort -V) )
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cp ${psfs[1]} ${out_dir}/combined/${system}-${concat_sel_s}.psf
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cp ${pdbs[1]} ${out_dir}/combined/${system}-${concat_sel_s}.pdb
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# ALIGN
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echo "set ref [atomselect top \""${align_sel}"\" frame 0]" >> temp.tcl
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echo "set sel [atomselect top \""${align_sel}"\"]" >> temp.tcl
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echo 'set all [atomselect top "all"]' >> temp.tcl
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echo 'set n [molinfo top get numframes]' >> temp.tcl
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echo 'for { set i 1 } { $i < $n } { incr i } {' >> temp.tcl
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echo ' $sel frame $i' >> temp.tcl
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echo ' $all frame $i' >> temp.tcl
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echo ' $all move [measure fit $sel $ref]' >> temp.tcl
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echo '}' >> temp.tcl
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# write aligned trr and dcd output files
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echo "animate write trr ${out_dir}/combined/${system}-${concat_sel_s}.trr waitfor all" >> temp.tcl
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echo "animate write dcd ${out_dir}/combined/${system}-${concat_sel_s}.dcd waitfor all" >> temp.tcl
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echo 'sync' >> temp.tcl
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echo 'exit' >> temp.tcl
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vmd -dispdev text -eofexit ${out_dir}/combined/${system}-${concat_sel_s}.psf ${dcds[@]} < "temp.tcl"
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rm "temp.tcl"
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sync
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done
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}
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#######################################################################################
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## CONCATENATE AND ALIGN ALL SYSTEMS (EDA) ##
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#######################################################################################
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function concat_eda() {
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get_systems
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mkdir -p ${out_dir}/eda/
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# concat systems to eda_sel
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for system in ${systems[@]}; do
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echo "set out [atomselect top \""${eda_sel}"\"]" > temp.tcl
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echo "set last_out [atomselect top \""${eda_sel}"\" frame 0]" >> temp.tcl
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# write aligned dcd
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echo "animate write dcd ${out_dir}/eda/${system}-${eda_sel_s}.dcd sel \$out waitfor all" >> temp.tcl
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echo "\$last_out writepsf ${out_dir}/eda/${system}-${eda_sel_s}.psf" >> temp.tcl
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echo "\$last_out writepdb ${out_dir}/eda/${system}-${eda_sel_s}.pdb" >> temp.tcl
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echo 'sync' >> temp.tcl
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echo 'exit' >> temp.tcl
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vmd -dispdev text -eofexit ${out_dir}/combined/${system}-${concat_sel_s}.psf ${out_dir}/combined/${system}-${concat_sel_s}.dcd < "temp.tcl"
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sync
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rm "temp.tcl"
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done
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dcds=( $(ls ${out_dir}/eda/*-${eda_sel_s}.dcd | sort -V) )
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psfs=( $(ls ${out_dir}/eda/*-${eda_sel_s}.psf | sort -V) )
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pdbs=( $(ls ${out_dir}/eda/*-${eda_sel_s}.pdb | sort -V) )
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cp ${psfs[1]} ${out_dir}/eda/combined-${eda_sel_s}.psf
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cp ${pdbs[1]} ${out_dir}/eda/combined-${eda_sel_s}.pdb
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# concat and align
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echo "set ref [atomselect top \""${eda_sel}"\" frame 0]" > temp.tcl
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echo "set sel [atomselect top \""${eda_sel}"\"]" >> temp.tcl
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echo 'set all [atomselect top "all"]' >> temp.tcl
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echo 'set n [molinfo top get numframes]' >> temp.tcl
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echo 'for { set i 1 } { $i < $n } { incr i } {' >> temp.tcl
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echo ' $sel frame $i' >> temp.tcl
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echo ' $all frame $i' >> temp.tcl
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echo ' $all move [measure fit $sel $ref]' >> temp.tcl
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echo '}' >> temp.tcl
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echo "animate write dcd ${out_dir}/eda/combined-${eda_sel_s}.dcd waitfor all" >> temp.tcl
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echo 'sync' >> temp.tcl
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echo 'exit' >> temp.tcl
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vmd -dispdev text -eofexit ${out_dir}/eda/combined-${eda_sel_s}.psf ${dcds[@]} < "temp.tcl"
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sync
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rm temp.tcl
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for system in ${systems[@]}; do
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rm "${out_dir}/eda/${system}-${eda_sel_s}.dcd"
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rm "${out_dir}/eda/${system}-${eda_sel_s}.pdb"
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rm "${out_dir}/eda/${system}-${eda_sel_s}.psf"
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done
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}
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concat_individual
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#concat_combined
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#concat_eda
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