RMSD problem

GROMACS version: 2020
GROMACS modification: No
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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.



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.

I see, thanks for clarifying.