auto_namd initial commit
This commit is contained in:
cryobry
441
auto_namd/functions.sh
Executable file
441
auto_namd/functions.sh
Executable file
@@ -0,0 +1,441 @@
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#!/usr/bin/env bash
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function get_next_step() {
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# get system name from path
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system=$(basename "${job}")
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# get prev_step and prev_step_num from parsing coor filenames
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last_step_coorname=$(find ${job} -name "*.coor" -type f | sort -V | tail -n 1)
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if [[ "${last_step_coorname}" == "" ]]; then
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prev_step=""
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else
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filename=$(basename ${last_step_coorname})
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filename=${filename%%.*}
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prev_step=${filename##${system}_}
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prev_step=${prev_step%%_*}
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fi
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case "${prev_step}" in
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"4-sim")
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this_step="4-sim"
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prev_step_num=${filename##*[^0-9]}
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final_step_num=$((${prev_step_num}+${step_size}))
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;;
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"3-heat")
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this_step="4-sim"
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prev_step_num=0
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final_step_num=${step_size}
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;;
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"2-min")
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this_step="3-heat"
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prev_step_num=0
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final_step_num=0
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;;
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"1-min")
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this_step="2-min"
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prev_step_num=0
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final_step_num=0
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;;
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"")
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if [[ -f "${job}/${system}.pdb" && -f "${job}/${system}.psf" ]]; then
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this_step="1-min"
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prev_step_num=0
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final_step_num=0
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else
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echo "No requisite pdb or psf files, exiting..."
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exit 1
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fi
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;;
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esac
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}
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function create_conf() {
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step_size=$((${final_step_num} - ${prev_step_num}))
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echo "Creating conf file using job:"${job}" system:"${system}" this_step:"$this_step" prev_step:$prev_step_num final_step:$final_step_num"
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#######################################################################################
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## CREATE NAMD CONFIGURATION FILES ##
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#######################################################################################
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case "${this_step}" in
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##########################
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## MINIMIZATION 1 ##
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##########################
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"1-min")
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conf="${job}/${system}_${this_step}.conf"
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out="${job}/${system}_${this_step}.out"
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echo "structure ${system}.psf" > ${conf}
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echo "coordinates ${system}.pdb" >> ${conf}
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echo "paraTypeCharmm on" >> ${conf}
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for ff in "${ffs[@]}"; do
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echo "parameters "${ff}"" >> ${conf}
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done
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echo "temperature 0" >> ${conf}
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echo "" >> ${conf}
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echo "# Force-Field Parameters" >> ${conf}
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echo "exclude scaled1-4" >> ${conf}
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echo "1-4scaling 1.0" >> ${conf}
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echo "cutoff 12." >> ${conf}
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echo "switching on" >> ${conf}
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echo "switchdist 10." >> ${conf}
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echo "pairlistdist 14" >> ${conf}
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echo "" >> ${conf}
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echo "# Integrator Parameters" >> ${conf}
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echo "timestep 1.0 ;# 1fs/step" >> ${conf}
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echo "nonbondedFreq 1" >> ${conf}
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echo "fullElectFrequency 2" >> ${conf}
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echo "stepspercycle 10" >> ${conf}
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echo "" >> ${conf}
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echo "# Output" >> ${conf}
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echo "outputName ${system}_${this_step}" >> ${conf}
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echo "outputEnergies 100" >> ${conf}
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echo "outputPressure 100" >> ${conf}
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# Minimize
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echo "minimize 15000" >> ${conf}
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;;
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##########################
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## MINIMIZATION 2 ##
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##########################
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"2-min")
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conf="${job}/${system}_${this_step}.conf"
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out="${job}/${system}_${this_step}.out"
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# Solvate and ionize
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solv_ion
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# create pcell.txt
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calc_pcell_min2
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# Source pcell.txt for PBC values
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source "${job}/${system}_${this_step}_pcell.txt"
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# Begin writing NAMD conf file
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echo "structure ${system}_solv_ion.psf" > ${conf}
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echo "coordinates ${system}_solv_ion.pdb" >> ${conf}
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echo "paraTypeCharmm on" >> ${conf}
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for ff in "${ffs[@]}"; do
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echo "parameters "${ff}"" >> ${conf}
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done
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echo "temperature 0" >> ${conf}
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echo "" >> ${conf}
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echo "# Periodic boundary conditions" >> ${conf}
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echo "wrapWater on" >> ${conf}
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echo "wrapAll on" >> ${conf}
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echo "cellOrigin $CORX $CORY $CORZ" >> ${conf}
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echo "cellBasisVector1 $CBVX 0.0 0.0" >> ${conf}
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echo "cellBasisVector2 0.0 $CBVY 0.0" >> ${conf}
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echo "cellBasisVector3 0.0 0.0 $CBVZ" >> ${conf}
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echo "# Force-Field Parameters" >> ${conf}
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echo "exclude scaled1-4" >> ${conf}
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echo "1-4scaling 1.0" >> ${conf}
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echo "cutoff 12." >> ${conf}
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echo "switching on" >> ${conf}
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echo "switchdist 10." >> ${conf}
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echo "pairlistdist 14" >> ${conf}
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echo "" >> ${conf}
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echo "# Integrator Parameters" >> ${conf}
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echo "timestep 2.0 ;# 2fs/step" >> ${conf}
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echo "rigidBonds all ;# needed for 2fs steps" >> ${conf}
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echo "nonbondedFreq 1" >> ${conf}
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echo "fullElectFrequency 2" >> ${conf}
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echo "stepspercycle 10" >> ${conf}
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echo "" >> ${conf}
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echo "# Output" >> ${conf}
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echo "outputName ${system}_${this_step}" >> ${conf}
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echo "outputEnergies 10000" >> ${conf}
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echo "outputPressure 10000" >> ${conf}
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# Minimize
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echo "minimize 15000" >> ${conf}
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;;
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##########################
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## EQUILIBRATION ##
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##########################
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"3-heat")
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conf="${job}/${system}_${this_step}.conf"
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out="${job}/${system}_${this_step}.out"
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# create pcell.txt
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calc_pcell_heat
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# Source pcell.txt for PBC values
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source "${job}/${system}_${this_step}_pcell.txt"
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echo "structure ${system}_solv_ion.psf" > ${conf}
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echo "coordinates ${system}_solv_ion.pdb" >> ${conf}
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echo "bincoordinates ${system}_2-min.coor" >> ${conf}
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echo "#extendedSystem ${system}_2-min.xsc" >> ${conf}
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echo "cellOrigin $CORX $CORY $CORZ" >> ${conf}
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echo "cellBasisVector1 $CBVX 0.0 0.0" >> ${conf}
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echo "cellBasisVector2 0.0 $CBVY 0.0" >> ${conf}
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echo "cellBasisVector3 0.0 0.0 $CBVZ" >> ${conf}
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echo "" >> ${conf}
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echo "firsttimestep ${prev_step_num}" >> ${conf}
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echo "" >> ${conf}
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echo "paraTypeCharmm on" >> ${conf}
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for ff in "${ffs[@]}"; do
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echo "parameters "${ff}"" >> ${conf}
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done
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echo "temperature 0" >> ${conf}
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echo "#margin 2" >> ${conf}
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echo "" >> ${conf}
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echo "# Periodic boundary conditions" >> ${conf}
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echo "wrapWater on" >> ${conf}
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echo "wrapAll on" >> ${conf}
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echo "" >> ${conf}
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echo "# Full Electrostatics" >> ${conf}
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echo "PME on" >> ${conf}
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echo "PMEGridSpacing 1.0" >> ${conf}
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echo "# Force-Field Parameters" >> ${conf}
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echo "exclude scaled1-4" >> ${conf}
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echo "1-4scaling 1.0" >> ${conf}
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echo "cutoff 12." >> ${conf}
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echo "switching on" >> ${conf}
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echo "switchdist 10." >> ${conf}
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echo "pairlistdist 14" >> ${conf}
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echo "" >> ${conf}
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echo "# Integrator Parameters" >> ${conf}
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echo "timestep 2.0 ;# 2fs/step" >> ${conf}
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echo "rigidBonds all ;# needed for 2fs steps" >> ${conf}
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echo "nonbondedFreq 1" >> ${conf}
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echo "fullElectFrequency 2 " >> ${conf}
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echo "stepspercycle 10" >> ${conf}
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echo "" >> ${conf}
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echo "# Output" >> ${conf}
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echo "outputName ${system}_${this_step}" >> ${conf}
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echo "outputEnergies 1000" >> ${conf}
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echo "outputPressure 1000" >> ${conf}
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echo "dcdfreq 1000" >> ${conf}
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echo "" >> ${conf}
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echo "# Constant Temperature Control" >> ${conf}
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echo "langevin on ;# do langevin dynamics" >> ${conf}
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echo "langevinDamping 0.5 ;# damping coefficient (gamma) of 0.5/ps" >> ${conf}
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echo "langevinTemp 310" >> ${conf}
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echo "langevinHydrogen no ;# don't couple langevin bath to hydrogens" >> ${conf}
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echo "" >> ${conf}
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echo "# Constant Pressure Control (variable volume)" >> ${conf}
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echo "useGroupPressure yes ;# needed for 2fs steps" >> ${conf}
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echo "useFlexibleCell yes ;# no for water box, yes for membrane" >> ${conf}
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echo "useConstantRatio yes ;# no for water box, yes for membrane" >> ${conf}
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echo "langevinPiston on" >> ${conf}
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echo "langevinPistonTarget 1.01325 ;# in bar -> 1 atm" >> ${conf}
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echo "langevinPistonPeriod 100." >> ${conf}
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echo "langevinPistonDecay 50." >> ${conf}
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echo "langevinPistonTemp 310" >> ${conf}
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echo "" >> ${conf}
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# Equilibration loop
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echo "set freq 100" >> ${conf}
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echo 'for {set i 10} {$i <= 310} {incr i 10} {' >> ${conf}
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echo 'reinitvels $i' >> ${conf}
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echo 'langevinTemp $i' >> ${conf}
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echo 'run $freq' >> ${conf}
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echo '}' >> ${conf}
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# Stabilize
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echo 'run 10000' >> ${conf}
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;;
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##########################
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## SIMULATION ##
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##########################
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"4-sim")
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conf="${job}/${system}_${this_step}_${final_step_num}.conf"
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out="${job}/${system}_${this_step}_${final_step_num}.out"
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# Begin writing NAMD conf file
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echo "structure ${system}_solv_ion.psf" > ${conf}
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echo "coordinates ${system}_solv_ion.pdb" >> ${conf}
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# if this is the first timestep, begin with heat
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if [[ ${prev_step_num} == 0 ]]; then
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echo "temperature 310" >> ${conf}
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echo "bincoordinates ${system}_3-heat.coor" >> ${conf}
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# create pcell.txt
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calc_pcell_heat
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source "${job}/${system}_${this_step}_pcell.txt"
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echo "cellOrigin $CORX $CORY $CORZ" >> ${conf}
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echo "cellBasisVector1 $CBVX 0.0 0.0" >> ${conf}
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echo "cellBasisVector2 0.0 $CBVY 0.0" >> ${conf}
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echo "cellBasisVector3 0.0 0.0 $CBVZ" >> ${conf}
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# else resume
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else
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echo "binvelocities ${system}_${this_step}_${prev_step_num}.vel" >> ${conf}
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echo "bincoordinates ${system}_${this_step}_${prev_step_num}.coor" >> ${conf}
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echo "extendedSystem ${system}_${this_step}_${prev_step_num}.xsc" >> ${conf}
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fi
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echo "" >> ${conf}
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echo "firsttimestep ${prev_step_num}" >> ${conf}
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echo "" >> ${conf}
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echo "#margin 2" >> ${conf}
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echo "paraTypeCharmm on" >> ${conf}
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for ff in "${ffs[@]}"; do
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echo "parameters "${ff}"" >> ${conf}
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done
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echo "" >> ${conf}
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echo "# Periodic boundary conditions" >> ${conf}
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echo "wrapWater on" >> ${conf}
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echo "wrapAll on" >> ${conf}
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echo "" >> ${conf}
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echo "# Full Electrostatics" >> ${conf}
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echo "PME on" >> ${conf}
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echo "PMEGridSpacing 1.0" >> ${conf}
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echo "" >> ${conf}
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echo "# Force-Field Parameters" >> ${conf}
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echo "exclude scaled1-4" >> ${conf}
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echo "1-4scaling 1.0" >> ${conf}
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echo "cutoff 12." >> ${conf}
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echo "switching on" >> ${conf}
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echo "switchdist 10." >> ${conf}
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echo "pairlistdist 14" >> ${conf}
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echo "" >> ${conf}
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echo "# Integrator Parameters" >> ${conf}
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echo "timestep 2.0 ;# 2fs/step" >> ${conf}
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echo "rigidBonds all ;# needed for 2fs steps" >> ${conf}
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echo "nonbondedFreq 1" >> ${conf}
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echo "fullElectFrequency 2 " >> ${conf}
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echo "stepspercycle 10" >> ${conf}
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echo "" >> ${conf}
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echo "# Output" >> ${conf}
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echo "outputName ${system}_${this_step}_${final_step_num}" >> ${conf}
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echo "outputEnergies 10000" >> ${conf}
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echo "outputPressure 10000" >> ${conf}
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echo "dcdfreq 10000" >> ${conf}
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echo "" >> ${conf}
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echo "# Constant Temperature Control" >> ${conf}
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echo "langevin on ;# do langevin dynamics" >> ${conf}
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echo "langevinDamping 0.5 ;# damping coefficient (gamma) of 0.5/ps" >> ${conf}
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echo "langevinTemp 310" >> ${conf}
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echo "langevinHydrogen no ;# don't couple langevin bath to hydrogens" >> ${conf}
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echo "" >> ${conf}
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echo "# Constant Pressure Control (variable volume)" >> ${conf}
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echo "useGroupPressure yes ;# needed for 2fs steps" >> ${conf}
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echo "useFlexibleCell yes ;# no for water box, yes for membrane" >> ${conf}
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echo "useConstantRatio yes ;# no for water box, yes for membrane" >> ${conf}
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echo "langevinPiston on" >> ${conf}
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echo "langevinPistonTarget 1.01325 ;# in bar -> 1 atm" >> ${conf}
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echo "langevinPistonPeriod 100." >> ${conf}
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echo "langevinPistonDecay 50." >> ${conf}
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echo "langevinPistonTemp 310" >> ${conf}
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echo "" >> ${conf}
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echo "run ${step_size}" >> ${conf}
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;;
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esac
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}
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function solv_ion() {
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# Create temporary VMD script to solvate, ionize, and generate PBC measurements
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# Load molecule
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echo "mol load psf [glob ${job}/${system}.psf] namdbin [glob ${job}/${system}_${prev_step}.coor]" > ${job}/temp_solv_ion.tcl
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echo "set all [atomselect top all]" >> ${job}/temp_solv_ion.tcl
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echo "\$all writepdb ${job}/${system}_${prev_step}.pdb" >> ${job}/temp_solv_ion.tcl
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# Solvate
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echo "package require solvate" >> ${job}/temp_solv_ion.tcl
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echo "solvate ${job}/${system}.psf ${job}/${system}_${prev_step}.pdb -o ${job}/${system}_solv -s WT -x 13 -y 13 -z 13 +x 13 +y 13 +z 13 -b 2.4" >> ${job}/temp_solv_ion.tcl
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# Ionize
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echo "package require autoionize" >> ${job}/temp_solv_ion.tcl
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echo "autoionize -psf ${job}/${system}_solv.psf -pdb ${job}/${system}_solv.pdb -o ${job}/${system}_solv_ion -sc 0.15" >> ${job}/temp_solv_ion.tcl
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# Run VMD
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vmd -dispdev text -eofexit < "${job}/temp_solv_ion.tcl"
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rm ${job}/temp_solv_ion.tcl
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}
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function calc_pcell_min2() {
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# Load molecule
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echo "mol load psf [glob ${job}/${system}_solv_ion.psf] pdb [glob ${job}/${system}_solv_ion.pdb]" > ${job}/temp_build_box.tcl
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# Get PBC box measurements from VMD and output to pcell.txt
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echo "set fileId [open ${job}/${system}_${this_step}_pcell.txt "w"]" >> ${job}/temp_build_box.tcl
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echo "set all [atomselect top "not lipid"]" >> ${job}/temp_build_box.tcl
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echo 'set minmax [measure minmax $all]' >> ${job}/temp_build_box.tcl
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echo 'set vec [vecsub [lindex $minmax 1] [lindex $minmax 0]]' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "#!/usr/bin/env bash"' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CBVX=[lindex $vec 0]"' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CBVY=[lindex $vec 1]"' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CBVZ=[lindex $vec 2]"' >> ${job}/temp_build_box.tcl
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echo 'set center [measure center $all]' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CORX=[lindex $center 0]"' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CORY=[lindex $center 1]"' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CORZ=[lindex $center 2]"' >> ${job}/temp_build_box.tcl
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echo 'close $fileId' >> ${job}/temp_build_box.tcl
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# Run VMD
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vmd -dispdev text -eofexit < "${job}/temp_build_box.tcl"
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rm "${job}/temp_build_box.tcl"
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}
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function calc_pcell_heat() {
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# Load molecule
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echo "mol load psf [glob ${job}/${system}_solv_ion.psf] namdbin [glob ${job}/${system}_${prev_step}.coor]" > ${job}/temp_build_box.tcl
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# Get PBC box measurements from VMD and output to pcell.txt
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echo "set fileId [open ${job}/${system}_${this_step}_pcell.txt "w"]" >> ${job}/temp_build_box.tcl
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echo "set all [atomselect top all]" >> ${job}/temp_build_box.tcl
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echo 'set minmax [measure minmax $all]' >> ${job}/temp_build_box.tcl
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echo 'set vec [vecsub [lindex $minmax 1] [lindex $minmax 0]]' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "#!/usr/bin/env bash"' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CBVX=[lindex $vec 0]"' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CBVY=[lindex $vec 1]"' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CBVZ=[lindex $vec 2]"' >> ${job}/temp_build_box.tcl
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echo 'set center [measure center $all]' >> ${job}/temp_build_box.tcl
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||||
echo 'puts $fileId "CORX=[lindex $center 0]"' >> ${job}/temp_build_box.tcl
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||||
echo 'puts $fileId "CORY=[lindex $center 1]"' >> ${job}/temp_build_box.tcl
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echo 'puts $fileId "CORZ=[lindex $center 2]"' >> ${job}/temp_build_box.tcl
|
||||
echo 'close $fileId' >> ${job}/temp_build_box.tcl
|
||||
|
||||
# Run VMD
|
||||
vmd -dispdev text -eofexit < "${job}/temp_build_box.tcl"
|
||||
rm "${job}/temp_build_box.tcl"
|
||||
}
|
||||
|
||||
function calc_pcell_sim() {
|
||||
# Load molecule
|
||||
echo "mol load psf [glob ${job}/${system}_solv_ion.psf] namdbin [glob ${job}/${system}_${prev_step}_${prev_step_num}.coor]" > ${job}/temp_build_box.tcl
|
||||
|
||||
# Get PBC box measurements from VMD and output to pcell.txt
|
||||
echo "set fileId [open ${job}/${system}_${this_step}_${prev_step_num}_pcell.txt "w"]" >> ${job}/temp_build_box.tcl
|
||||
echo "set all [atomselect top all]" >> ${job}/temp_build_box.tcl
|
||||
echo 'set minmax [measure minmax $all]' >> ${job}/temp_build_box.tcl
|
||||
echo 'set vec [vecsub [lindex $minmax 1] [lindex $minmax 0]]' >> ${job}/temp_build_box.tcl
|
||||
echo 'puts $fileId "#!/usr/bin/env bash"' >> ${job}/temp_build_box.tcl
|
||||
echo 'puts $fileId "CBVX=[lindex $vec 0]"' >> ${job}/temp_build_box.tcl
|
||||
echo 'puts $fileId "CBVY=[lindex $vec 1]"' >> ${job}/temp_build_box.tcl
|
||||
echo 'puts $fileId "CBVZ=[lindex $vec 2]"' >> ${job}/temp_build_box.tcl
|
||||
echo 'set center [measure center $all]' >> ${job}/temp_build_box.tcl
|
||||
echo 'puts $fileId "CORX=[lindex $center 0]"' >> ${job}/temp_build_box.tcl
|
||||
echo 'puts $fileId "CORY=[lindex $center 1]"' >> ${job}/temp_build_box.tcl
|
||||
echo 'puts $fileId "CORZ=[lindex $center 2]"' >> ${job}/temp_build_box.tcl
|
||||
echo 'close $fileId' >> ${job}/temp_build_box.tcl
|
||||
|
||||
# Run VMD
|
||||
vmd -dispdev text -eofexit < "${job}/temp_build_box.tcl"
|
||||
rm "${job}/temp_build_box.tcl"
|
||||
}
|
||||
|
||||
function copy_ffs() {
|
||||
ffs=()
|
||||
for ff in ../0-forcefields/*; do
|
||||
if [[ -f "${ff}" ]]; then
|
||||
# strip path
|
||||
ff_name=${ff##*/}
|
||||
# copy ff and append to ffs array
|
||||
cp -f "${ff}" "${job}/${ff_name}"
|
||||
ffs+=(${ff##*/})
|
||||
fi
|
||||
done
|
||||
}
|
||||
|
||||
function backup() {
|
||||
if [[ -f "${out}" ]]; then
|
||||
mv "${out}" "${out}.bak"
|
||||
fi
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user