#!/bin/sh

here=`pwd`
here=`basename $here`
dir="/home/mnelson/struct_calc/amber/$here"

files=`ls f36g???.xyz`

for file in $files
do
   file=`echo $file | sed -e 's/f36g//'`
   file=`echo $file | sed -e 's/\.xyz//'`
echo "#!/bin/sh" > anneal$file
echo "" >> anneal$file
echo "MP_SET_NUMTHREADS=1" >> anneal$file
echo "export MP_SET_NUMTHREADS" >> anneal$file
echo "" >> anneal$file
echo "cd $dir" >> anneal$file
echo "" >> anneal$file
echo "files=\"\\" >> anneal$file
echo "f36g$file.xyz \\" >> anneal$file
echo "\"" >> anneal$file
echo "" >> anneal$file
echo "for file in \$files" >> anneal$file
echo "do" >> anneal$file
echo "   input=\`echo \$file | sed -e 's/\..*$//'\`" >> anneal$file
echo "" >> anneal$file
echo "cat <<eof > \${input}min.in" >> anneal$file
echo "  minimization with constraints" >> anneal$file
echo "" >> anneal$file
echo "# energy minimization protocol" >> anneal$file
echo "" >> anneal$file
echo " &cntrl" >> anneal$file
echo "    maxcyc=5000, pencut=0.1, nmrmax=1, imin=1," >> anneal$file
echo "    temp0 = 0.5, tautp=0.02, ntpr=50, ntt=1," >> anneal$file
echo "    nsnb=50, cut=8.0, idiel=0, scnb=2.0, scee=2.0," >> anneal$file
echo " &end" >> anneal$file
echo " &wt type='END'  &end" >> anneal$file
echo "DISANG=f36g.min.RST" >> anneal$file
echo "LISTOUT=POUT" >> anneal$file
echo "eof" >> anneal$file
echo "" >> anneal$file
echo "cat <<eof > \${input}rmd.in" >> anneal$file
echo "  simulated annealing" >> anneal$file
echo "" >> anneal$file
echo "# simulated annealing protocol" >> anneal$file
echo " &cntrl" >> anneal$file
echo "    nstlim=20000, pencut=0.1, nmrmax=1," >> anneal$file
echo "    temp0 = 0.5, tautp=0.02, ntpr=200, ntt=1," >> anneal$file
echo "    nsnb=50, cut=8.0, idiel=0, scnb=2.0, scee=2.0," >> anneal$file
echo " &end" >> anneal$file
echo "" >> anneal$file
echo "#Simple simulated annealing algorithm:" >> anneal$file
echo "" >> anneal$file
echo "#From steps 1 to 1000: use initial values of temp0 and tautp, which" >> anneal$file
echo "#    will effective minimize the energy;" >> anneal$file
echo "#from steps 1000 to 5000: heat the system to 1200K with a slower" >> anneal$file
echo "#    temperature coupling paramter:" >> anneal$file
echo "#from steps 5000-9000: re-cool to low temperatures" >> anneal$file
echo "#from steps 9000-10000: final cooling with short tautp" >> anneal$file
echo "" >> anneal$file
echo " &wt type='TEMP0', istep1=0,istep2=10000,value1=1200.," >> anneal$file
echo "            value2=1200.,    &end" >> anneal$file
echo " &wt type='TEMP0', istep1=10001, istep2=12000, value1=1200.," >> anneal$file
echo "            value2=0.0,     &end" >> anneal$file
echo " &wt type='TEMP0', istep1=12001, istep2=20000, value1=0.," >> anneal$file
echo "            value2=0.0,     &end" >> anneal$file
echo "" >> anneal$file
echo " &wt type='TAUTP', istep1=0,istep2=4000,value1=0.2," >> anneal$file
echo "            value2=0.2,     &end" >> anneal$file
echo " &wt type='TAUTP', istep1=4001,istep2=10000,value1=0.5," >> anneal$file
echo "            value2=0.2,     &end" >> anneal$file
echo " &wt type='TAUTP', istep1=10001,istep2=17000,value1=1.2," >> anneal$file
echo "            value2=1.2,     &end" >> anneal$file
echo " &wt type='TAUTP', istep1=17001,istep2=19000,value1=0.5," >> anneal$file
echo "            value2=0.5,     &end" >> anneal$file
echo " &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.05," >> anneal$file
echo "            value2=0.05,     &end" >> anneal$file
echo "" >> anneal$file
echo "#Turn the NMR restraints on slowly during the first 3000 steps." >> anneal$file
echo "" >> anneal$file
echo " &wt type='REST', istep1=0, istep2=2000, value1=0.0," >> anneal$file
echo "            value2=1.0,     &end" >> anneal$file
echo " &wt type='REST', istep1=2001, istep2=10000, value1=1.0," >> anneal$file
echo "            value2=1.0,     &end" >> anneal$file
echo "" >> anneal$file
echo " &wt type='END'  &end" >> anneal$file
echo "DISANG=f36g.RST" >> anneal$file
echo "LISTOUT=POUT" >> anneal$file
echo "eof" >> anneal$file
echo "" >> anneal$file
echo "   /home/mnelson/bin/md/sander.a5 -O \\" >> anneal$file
echo "         -i \${input}min.in \\" >> anneal$file
echo "         -p prmtop.leap91 \\" >> anneal$file
echo "         -c \$input.xyz \\" >> anneal$file
echo "         -inf monmin.\$input.info \\" >> anneal$file
echo "         -o monmin.\$input.out \\" >> anneal$file
echo "         -r monmin.\$input.xyz" >> anneal$file
echo "   /bin/rm \${input}min.in" >> anneal$file
echo "   /bin/rm monmin.\$input.info" >> anneal$file
echo "   /home/mnelson/bin/md/sander.a5 -O \\" >> anneal$file
echo "         -i \${input}rmd.in \\" >> anneal$file
echo "         -p prmtop.leap91 \\" >> anneal$file
echo "         -c monmin.\$input.xyz \\" >> anneal$file
echo "         -inf monrmd.\$input.info \\" >> anneal$file
echo "         -o monrmd.\$input.out \\" >> anneal$file
echo "         -r monrmd.\$input.xyz" >> anneal$file
echo "   /bin/rm \${input}rmd.in" >> anneal$file
echo "   /bin/rm monrmd.\$input.info" >> anneal$file
echo "" >> anneal$file
echo "   /bin/rm monmin.\$input.out" >> anneal$file
echo "   /bin/rm monmin.\$input.xyz" >> anneal$file
echo "done" >> anneal$file

chmod 755 anneal$file
done