<div>Thankyou Justin for your suggestion</div>
<div><br>I tried this command---></div>
<div> </div>
<div>trjconv -f myprotein.trr -o trajout_whole.trr -pbc whole</div>
<div> </div>
<div> this was showing this error</div>
<div> </div>
<div> "can not open file</div>
<div> topol.tpr"</div>
<div> then</div>
<div>I repeated the same command with "-s topol.tpr"</div>
<div> </div>
<div>then</div>
<div> </div>
<div>trjconv -f trajout_whole.trr -o trajout_nojump.trr -pbc nojump</div>
<div> </div>
<div>then</div>
<div> </div>
<div>g_rms -s topol.tpr -f trajout_nojump.trr -o trajout_nojump_rmsd.xvg -xvgr</div>
<div> </div>
<div>but now this is showing Fatal Error</div>
<div> </div>
<div>" 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."</div>
<div> </div>
<div>with regards</div>
<div> Anamika</div>
<div> </div>
<div> <br></div>