RMSD without alignment?

[Glen Hocky]

Dear PLUMED friends,

We are studying a protein complex, and we're interested in computing a distance between the current domain configuration in simulation with respect to that in a reference structure. What we would like to do is e.g. align domain B in the protein to the reference (i.e. FIT_TO_TEMPLATE) and then compute RMSD of domain A to itself without additional alignment. 

Has anyone done that before? Would it be as simple as adding an option to not align in the RMSD command?

Thanks for your help,

Glen

p.s. We see that there used to be a function TARGET which is like this, but which has been removed. This might work but explicit lists of pairwise distances must be constructed. We also observe that there is an INTER version of DMRSD now, which also potentially achieve the same goal, by using DRMSD of domain A to other parts of the complex, but that would not be the same as RMSD of domain A to itself.

[Giovanni Bussi]

Hi Glen

Can you just use RMSD with different sets of atoms in the align and displace weights (two columns in the pdb file)?

If this works for you it will be also better implemented than fit to template in terms of performance

Giovanni

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