Dear Raza

I myself use Amber for simulation instead of MOE cause MOE is time taking software but I have attached document demonstrating various steps for calculating RMSD in MOE.

Regards!

Dear Muslim Raza Raza,

I never used MOE but you can try as follows.

You have to simply take the geometry files (xyz files) from the MD simulations with the corresponding time (using grep or whatever).

Firstly, I will recommend you VMD to do it by hand.

You can just upload few structures to VMD or the whole trajectory thorough Extensions/ Analysis/RMSD Calculator  or directly upload trajectory RMSD trajectory tool, more info you can find in the manual of AMBER package. 

Than you can make it throught VMD script: http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node4.html

Best regards,

Darek

Dear Raza

I myself use Amber for simulation instead of MOE cause MOE is time taking software but I have attached document demonstrating various steps for calculating RMSD in MOE.

Regards!