RMSD problem

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1

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.

Thanks,

Ben

2

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.

3

I see, thanks for clarifying.