#!/bin/sh /bin/rm -f md?_cpout.pH_2.00.gz EXE=../../bin/cphstats NFAIL=0 if [ ! -z "$1" -a "$1" = "clean" ]; then /bin/rm -f md?_cpout.pH_?.?? /bin/rm -f *.dat /bin/rm -f *.calcpka /bin/rm -f *.txt exit 0 fi if [ ! -x $EXE ]; then echo "Could not find cphstats in the previous directory." echo "Re-install, then test again." exit 1 fi # First unpack the REMD files $EXE -O --fix-remd md2_cpout pH*/1AKI.dry.md2.cpout $EXE -O --fix-remd md3_cpout pH*/1AKI.dry.md3.cpout # Diff some of them ../dacdif md2_cpout.pH_2.00.save md2_cpout.pH_2.00 ../dacdif md3_cpout.pH_4.50.save md3_cpout.pH_4.50 # Check the calcpka output $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_2.00 -o pH_2.00.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_2.50 -o pH_2.50.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_3.00 -o pH_3.00.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_3.50 -o pH_3.50.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 -o pH_4.00.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.50 -o pH_4.50.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_5.00 -o pH_5.00.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_5.50 -o pH_5.50.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_6.00 -o pH_6.00.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_6.50 -o pH_6.50.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_7.00 -o pH_7.00.calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_7.50 -o pH_7.50.calcpka ../dacdif -r 5e-1 pH_2.00.calcpka.save pH_2.00.calcpka ../dacdif -r 5e-1 pH_2.50.calcpka.save pH_2.50.calcpka ../dacdif -r 5e-1 pH_3.00.calcpka.save pH_3.00.calcpka ../dacdif -r 5e-1 pH_3.50.calcpka.save pH_3.50.calcpka ../dacdif -r 5e-1 pH_4.00.calcpka.save pH_4.00.calcpka ../dacdif -r 5e-1 pH_4.50.calcpka.save pH_4.50.calcpka ../dacdif -r 5e-1 pH_5.00.calcpka.save pH_5.00.calcpka ../dacdif -r 5e-1 pH_5.50.calcpka.save pH_5.50.calcpka ../dacdif -r 5e-1 pH_6.00.calcpka.save pH_6.00.calcpka ../dacdif -r 5e-1 pH_6.50.calcpka.save pH_6.50.calcpka ../dacdif -r 5e-1 pH_7.00.calcpka.save pH_7.00.calcpka ../dacdif -r 5e-1 pH_7.50.calcpka.save pH_7.50.calcpka # Check reading of gzipped cpouts for cpout in md?_cpout.pH_2.00; do gzip -9 $cpout done $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_2.00.gz -o pH_2.00.calcpka \ --debug > cphstats_output.txt ../dacdif -r 5e-1 pH_2.00.calcpka.save pH_2.00.calcpka ../dacdif -r 5e-1 cphstats_output.txt.save cphstats_output.txt # Check running averages $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ -r 100000 --no-calcpka -n 100 $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ -r 100000 -R running_avg.dat -d --no-calcpka -n 1000 $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ -r 100000 -R running_pKa.dat -a --no-calcpka -n 5000 ../dacdif -r 5e-1 running_avgs.dat.save running_avgs.dat ../dacdif -r 5e-1 running_avg.dat.save running_avg.dat ../dacdif -r 5e-1 running_pKa.dat.save running_pKa.dat # Check chunk averages $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ --chunk 1000000 --no-calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ --chunk 1000000 --chunk-out chunk_deprot.dat --no-calcpka -d $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ --chunk 1000000 --chunk-out chunk_pka.dat --no-calcpka -a ../dacdif -r 5e-1 chunk.dat.save chunk.dat ../dacdif -r 5e-1 chunk_deprot.dat.save chunk_deprot.dat ../dacdif -r 5e-1 chunk_pka.dat.save chunk_pka.dat # Check cumulative output $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ --cumulative --no-calcpka -n 1000 --no-calcpka $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ --cumulative --no-calcpka -n 1000 -d --no-calcpka \ --cumulative-out cumulative_deprot.dat $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ --cumulative --no-calcpka -n 1000 -a --no-calcpka \ --cumulative-out cumulative_pka.dat ../dacdif -r 5e-1 cumulative.dat.save cumulative.dat ../dacdif -r 5e-1 cumulative_deprot.dat.save cumulative_deprot.dat ../dacdif -r 5e-1 cumulative_pka.dat.save cumulative_pka.dat # Check the population output $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ --population pop.dat --no-calcpka ../dacdif -r 5e-1 pop.dat.save pop.dat # Check the conditional probability output $EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \ --no-calcpka -c 35:prot,52:0 -c 66:D,48:P \ --conditional-output conditional.dat \ --chunk-conditional conditional_chunks.dat ../dacdif -r 5e-1 conditional.dat.save conditional.dat ../dacdif -r 5e-1 conditional_chunks.dat.save conditional_chunks.dat