[gmx-users] abnormal RMSD

[Anamika Awasthi]

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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