[gmx-users] RMSD of the same protein in different solvent boxes

[Afonso Duarte]

Hi to All,

I have some simulations of the same protein in different solvents, with different number of atoms for each (different solvent number of atoms). 
I would like to calculate a rmsd matrix to compar the backbone of the different sims.

I have tried g_rms with the -f2 option to include the second trajectory, however it finishes with a fatal error because teh number of total atoms is different in both trajectories.

Does anybody know how to solve this question? Is it possible to produce the rmsd matrix in a different way?

Thanks in advance

Afonso

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