Re: RMSD collective variable - Different atons to align and to calculate RMSD

From: Paulo Cesar Telles de Souza (
Date: Tue Feb 07 2012 - 11:53:47 CST

Hello everyone

Thank you for answers. Sorry for being slow to answer, but I spent a
few days thinking about the considerations that you did. The problem
that occurred to me is that alignment problems may occur if the
conformation differences are great. With a bad alignment, the average
force at a given RMSD can be compromised. If I have to use the same
atoms in the current version of NAMD, then I will include a few others
that do not have large conformational differences in relation to the
references. So it is possible to prevent alignment problems to which I
What do you think about this option?



2012/2/2 Jérôme Hénin <>

> I concur with Chris. In some special cases I see why you might want to
> align some atoms and measure deviation on others, but not in the case
> you described.
> Best,
> Jerome
> On 2 February 2012 20:54, Chris Harrison <> wrote:
> > The are the same. It is not clear to me why you'd want to calc the RMSD
> of
> > a set of atoms which do not correspond to the subset used for alignment--f46d043c7dbe0247ee04b86376da--

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