apolar

NULL=0  
error=0

while true
do
    sleep 1
    if  [ -e MD_prep.out ]; then
        grep Error MD_prep.out > gromacs_errors
    fi

    if  [ -e MD_run.out ]; then
        grep Error MD_run.out >> gromacs_errors
    fi

    if  [ -e ndx.out ]; then
        grep Error ndx.out >> gromacs_errors
    fi

    if  [ -e ndx.error ]; then
        echo "ndx error" >> gromacs_errors
    fi

    nolines=`wc -l < gromacs_errors`
    if  [ $nolines -gt $NULL ]; then
        echo "one of gromacs jobs failed. exiting loop."
        error=1 ; break
    fi

    if  [ -e md_0_1.log ] #exit w/o error if MD_run job finished
    then
        grep Finished md_0_1.log > tmp
        if  [ -s tmp ]
        then
            error=0 ; break
        fi
    fi
done
rm -f end

if [ $error -eq $NULL ]
then
    while [ ! -e md_0_1.ndx ] #wait until ndx job finishes
    do
         sleep 1
    done
    echo 1 13 | g_mmpbsa -f md_0_1.xtc -s md_0_1.tpr -n md_0_1.ndx -i apolar_sasa.mdp -nomme -pbsa -decomp -apol sasa.xvg -apcon sasa_contrib.dat
fi