[gmx-users] regarding rmsd calculaton

[shakuntala dhurua]

actually I am using insulin protein system, i have calculated rmsd but that
is too high which is approx 40 amstrong which is not supposed to be , and
initially during energy minimization two chain go far away from each other.
I have used flag like trjconv -s .tpr -f .trr -o .xtc -pbc mol -ur compact
trjconv -s .tpr -f .trr -o .xtc -pbc nojump etc but still result is same .
so please suggest me to solve this problem.