[gmx-users] regarding rmsd calculaton

[rajat punia]

make sure you superimpose the structures using -fit flag.


On Wed, 30 Oct 2019 at 16:39, shakuntala dhurua <madhu.dhurua94 at gmail.com>
wrote:

> 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.
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-- 
*Regards,*
*Rajat Punia*
*PhD Chemical Engineering*
*IIT Delhi*
*+91-9821210386*