auto_namd initial commit

auto_namd/functions.sh

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

auto_namd/hosts.sh

@@ -0,0 +1,128 @@
+##########################################
+## HOSTNAMES                                                                               ##
+##########################################
+
+function run_cheaha() {
+  echo "#!/usr/bin/env bash" > temp_sbatch
+  echo "#SBATCH --ntasks=${ntasks}" >> temp_sbatch
+  echo "#SBATCH --partition=${partition}" >> temp_sbatch
+  echo "#SBATCH --time=${time}" >> temp_sbatch
+  echo "#SBATCH --mem-per-cpu=${mem_per_cpu}" >> temp_sbatch
+  echo "#SBATCH --nodes=${nodes}" >> temp_sbatch
+  echo "#SBATCH --job-name=${job}_${this_step}_${final_step_num}" >> temp_sbatch
+  echo '# Load module(s)' >> temp_sbatch
+  echo 'module load rc/NAMD/2.12' >> temp_sbatch
+
+  # generate temp NAMD nodelist
+  echo 'for n in `echo ${SLURM_NODELIST} | scontrol show hostnames`; do' >> temp_sbatch
+  echo '  echo "host $n ++cpus 24" >> ${TMPDIR}/nodelist.${SLURM_JOBID}' >> temp_sbatch
+  echo 'done' >> temp_sbatch
+
+  # calculate ppn
+  echo 'PPN=$(expr $SLURM_NTASKS / $SLURM_NNODES - 1)' >> temp_sbatch
+  echo 'P="$(($PPN * $SLURM_NNODES))"' >> temp_sbatch
+  
+  # find namd location
+  echo 'namd_bin="$(which namd2)"' >> temp_sbatch
+  
+  echo "$(echo "${namd_param}") ${conf} > ${out}" >> temp_sbatch
+  
+  # cleanup temp NAMD nodelist
+  echo 'rm ${TMPDIR}/nodelist.${SLURM_JOBID}' >> temp_sbatch
+  
+  # submit using sbatch
+  sbatch temp_sbatch
+  rm temp_sbatch
+}
+
+function run_workstation() {
+  $(echo "${namd_param}") ${conf} > ${out}
+ }
+ 
+function run_asc() {
+  job_name_pref=${job##*.}_${this_step}_${final_step_num}
+  
+  /apps/scripts/check_ssh
+  /apps/scripts/qquery program=namd input=$conf
+  
+  # create ~/.asc_queue
+  
+  echo 'start_time_pref=SOONEST' > ${HOME}/.asc_queue
+  echo "job_name_pref=${job_name_pref}" >> ${HOME}/.asc_queue
+  echo "queue_name_pref=${queue_name_pref}" >> ${HOME}/.asc_queue
+  echo "num_cpus_pref=${num_cpus_pref}" >> ${HOME}/.asc_queue
+  echo "cpu_time_pref=${cpu_time_pref}" >> ${HOME}/.asc_queue
+  echo "memory_pref=${memory_pref}" >> ${HOME}/.asc_queue
+  echo "cluster_pref=${cluster_pref}" >> ${HOME}/.asc_queue
+  
+  if [ -f qfile ]
+  then
+    read queue time memory sttime num_cpus < qfile
+    rm qfile
+  else
+    echo "ERROR: qfile not found"
+    echo "       Make sure you have write permissions in this directory"
+    exit
+  fi
+   
+  # get limits
+  limits=`/apps/scripts/set_limits $time $num_cpus NA $memory NA NA`
+  
+  # get qos
+  qos=`/apps/scripts/set_qos $queue`
+  
+  # get constraints
+  constraints="--constraint=dmc|uv"  # both clusters, not KNL
+  
+  echo '#!/usr/bin/env bash' > temp_sbatch
+  echo 'pwd="$(pwd)"' >> temp_sbatch
+  echo 'echo "pwd: $pwd"' >> temp_sbatch
+  echo '#  set the workdir variable' >> temp_sbatch
+  echo "export workdir=/scratch/${LOGNAME}/${job##*./}" >> temp_sbatch
+  echo 'echo "workdir: $workdir"' >> temp_sbatch
+  echo '# load modules' >> temp_sbatch
+  echo 'source /opt/asn/etc/asn-bash-profiles-special/modules.sh' >> temp_sbatch
+  echo 'module purge' >> temp_sbatch
+  echo 'if [ ! -d $workdir ]' >> temp_sbatch
+  echo 'then' >> temp_sbatch
+  echo '  mkdir -p $workdir' >> temp_sbatch
+  echo 'fi' >> temp_sbatch
+  echo 'export TEMPDIR=$workdir' >> temp_sbatch
+  echo 'export TMPDIR=$workdir' >> temp_sbatch
+  echo 'export CONV_RSH=ssh' >> temp_sbatch
+  echo '# run from the current directory' >> temp_sbatch
+  echo "./cp_wild_r $job \$workdir" >> temp_sbatch
+  echo 'sleep 15' >> temp_sbatch
+  echo 'cd $workdir' >> temp_sbatch
+  echo 'export uv_test=`hostname | grep uv | wc -l`' >> temp_sbatch
+  echo 'export dmc_test=`hostname | grep dmc | wc -l`' >> temp_sbatch
+  echo '# code for the DMC' >> temp_sbatch
+  echo 'if [ $dmc_test == "1" ]' >> temp_sbatch
+  echo 'then' >> temp_sbatch
+  echo '  module purge' >> temp_sbatch
+  echo '  module load namd/2.12_ibverbs' >> temp_sbatch
+  echo '  namd_bin="$(which namd2)"' >> temp_sbatch
+  echo '  # run NAMD' >> temp_sbatch
+  echo '  alias mpiexec="srun"' >> temp_sbatch
+  echo "  charmrun +p $num_cpus_pref ++mpiexec \${namd_bin} ${conf##*/} > ${out##*/}" >> temp_sbatch
+  echo 'fi' >> temp_sbatch
+  echo '# code for the UV' >> temp_sbatch
+  echo 'if [ "$uv_test" == "1" ]' >> temp_sbatch
+  echo 'then' >> temp_sbatch
+  echo '  module purge' >> temp_sbatch
+  echo '  module load namd/2.12' >> temp_sbatch
+  echo '  namd_bin="$(which namd2)"' >> temp_sbatch
+  echo '  # run NAMD' >> temp_sbatch
+  echo "  charmrun +p $num_cpus_pref \${namd_bin} ${conf##*/} > ${out##*/}" >> temp_sbatch
+  echo 'fi' >> temp_sbatch
+  echo 'sleep 10' >> temp_sbatch
+  echo 'cd ${pwd}' >> temp_sbatch
+  echo "./cp_wild_r \$workdir $job" >> temp_sbatch
+  echo 'sleep 15' >> temp_sbatch
+  echo 'rm -r $workdir' >> temp_sbatch
+  echo 'exit 0' >> temp_sbatch
+
+  sbatch $qos  -J $job_name_pref --begin=$sttime --requeue $limits $constraints temp_sbatch
+  rm temp_sbatch
+
+}

auto_namd/run.sh

@@ -0,0 +1,63 @@
+#!/usr/bin/env bash
+
+source ./functions.sh
+source ./hosts.sh
+
+# ADJUSTABLE PARAMETERS
+# set directory containing jobs to be run
+jobs=( "../4-jobs/18_04_02/5w81-swiss*/" )
+step_size=1000000
+#repeats=50
+
+
+# FUNCTIONS
+# remove trailing slashes from jobs array
+jobs=(${jobs[@]%/})
+
+
+# HOSTNAME PARAMETERS
+function run_namd() {
+  case "${HOSTNAME}" in
+    "phy145.physiology.uab.edu") # Workstation (local)
+      namd_param='/home/bryan/bin/namd/namd2 +p55 +idlepoll'
+      run_workstation
+      ;;
+    "login001") # Cheaha (Slurm)
+      namd_param='charmrun ++mpiexec ++nodelist ${TMPDIR}/nodelist.${SLURM_JOBID} +p ${SLURM_NTASKS} ${namd_bin}'
+      partition="short"
+      ntasks=96
+      nodes=4
+      time="12:00:00"
+      mem_per_cpu=128
+      run_cheaha
+      ;;
+    "uv.asc.edu") # ASC (Slurm script)
+      namd_param="runnamd"
+      queue_name_pref="large"
+      num_cpus_pref=64
+      cpu_time_pref="DEFAULT"
+      memory_pref="16gb"
+      cluster_pref='"uv|dmc"'
+      run_asc
+      ;;
+     *) # unknown
+       echo "You are running on an unknown system: \"${HOSTNAME}\"..."
+       echo "You must first add this machine to the resources section in run_namd.sh"
+       echo "Exiting..."
+       exit 1
+       ;;
+  esac
+}
+
+
+# RUN LOOP
+
+for r in {1..50}; do
+  for job in "${jobs[@]}"; do
+    get_next_step
+    copy_ffs
+    create_conf
+    backup
+    run_namd
+  done
+done