#to get ntotframes first

trjin file="step9_harvest.trj"

ifrm=0

while($ifrm<$ntotframes){

  trjreadnextframe

  mdtime=$curmdtime

  #double check whether trjreadnextframe successfully or not

  if($mdtime<0) abort

  #print progress for every 10ps

  tmod=$mdtime%10

  if($tmod==0) echo -hs "current MD time: $mdtime ps"

  #recalculate enerergy for each frame

  doenergy

  #calculate RMSD for all heavy atoms comparing to initial structure

  calc rmsd fitgroup=mainpro calcgroup=mainpro

  echo "$mdtime $value" >> rmsd.txt

  #calculate RMSD for main chain atoms

  calc rmsd fitgroup="mainpro and name C CA N O" \

            calcgroup="mainpro and name C CA N O"

  echo "$mdtime $value" >> mainrmsd.txt

  #calculate distance between terminals

  calc dist group1="residue PROA 41" group2="residue PROA 76"

  echo "$mdtime $value" >> dist.txt

  #calculate PHI,PSI for residue 50

  calc dihe group1="atom PROA 49 C" \

            group2="atom PROA 50 N" \

            group3="atom PROA 50 CA" \

            group4="atom PROA 50 C"

  phi=$value

  calc dihe group1="atom PROA 50 N" \

            group2="atom PROA 50 CA" \

            group3="atom PROA 50 C" \

            group4="atom PROA 51 N"

  psi=$value

  echo "$mdtime $PHI $PSI" >> phipsi.txt

  #calculate Radius of Gyration

  calc rgy  select="all"

  echo "$mdtime $value" >> rgy.txt

  ifrm=$ifrm+1

}