# RMSD problem **URL:** \ **Category:** User discussions\ **Created:** [June 1, 2021, 6:33am UTC](https://gromacs.bioexcel.eu/t/rmsd-problem/2263 "2021-06-01T06:33:35Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![btam125](https://avatars.discourse-cdn.com/v4/letter/b/a88e57/32.png) [@btam125](https://gromacs.bioexcel.eu/u/btam125)\ **Post date:** [June 1, 2021, 6:33am UTC](https://gromacs.bioexcel.eu/t/rmsd-problem/2263/1 "2021-06-01T06:33:35Z")
GROMACS version: 2020 GROMACS modification: No Here post your question Dear all, When I used RMSD to calculate a few simulations, some of them at 0 time frame, the RMSD is 0. While some of the simulation at 0 time frame, it starts with 0.8 nm and it decreases towards 0 during the simulation. Therefore, I just like to ask how come and why this happened? All the simulation had gone through steep run and same system conditions. Any help would be appreciated. Thanks, Ben ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [June 3, 2021, 1:07pm UTC](https://gromacs.bioexcel.eu/t/rmsd-problem/2263/2 "2021-06-03T13:07:26Z")
It depends on what you’re using as the reference coordinate file. If you’re using the frame at t = 0 (e.g. the equilibrated structure), you should get RMSD = 0 at t = 0 because they are the same structure. If you’re using the energy-minimized structure, the first RMSD value will likely be non-zero because even if you applied restraints during equilibration, the structure will move a bit. ---
**Author:** ![btam125](https://avatars.discourse-cdn.com/v4/letter/b/a88e57/32.png) [@btam125](https://gromacs.bioexcel.eu/u/btam125)\ **Post date:** [June 4, 2021, 2:21am UTC](https://gromacs.bioexcel.eu/t/rmsd-problem/2263/3 "2021-06-04T02:21:25Z")
I see, thanks for clarifying.