Thankyou Justin for your suggestion
I tried this command--->
trjconv -f myprotein.trr -o trajout_whole.trr -pbc whole
this was showing this error
"can not open file
topol.tpr"
then
I repeated the same command with "-s topol.tpr"
then
trjconv -f trajout_whole.trr -o trajout_nojump.trr -pbc nojump
then
g_rms -s topol.tpr -f trajout_nojump.trr -o trajout_nojump_rmsd.xvg -xvgr
but now this is showing Fatal Error
" Molecule in topology has atom numbers below and above natoms. you are
probably trying to use a trajectory which does not match the first 330 atoms
of the run input file. You can make a matching run input file with tpbconv."
with regards
Anamika
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