[gmx-users] Some confusion about calculation of RMSDs

[Marc Baaden]

Hi,

I just checked the RMSD definitions given in the Gromacs manual
and was a bit surprised to find that the mass-weighted RMSD is
the value calculated by default. I thought that by default RMSD
meant equal contribution of each atom you include in the calculation
*unless* you state/define otherwise. Is there any "standard" ?

Also I am a bit unsure about the fitting part. My guess would be
that fitting is equally weighted ? Or is it also mass-weighted ?

  Marc

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
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