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

From: Branko (
Date: Tue Feb 07 2012 - 12:49:37 CST


I didn't read your initial question, but it is very useful to read
numerical values
of RMSD (used as collective variable) from colvars trajectory file. From
time to time there can be significant discrepancies with RMSD of the
same atoms, if RMSD is 'read' from dcd (different GUI's used for dcd
analysis give almost identical results) and colvars trajectory. Also
consider that atom positions RMSD in colvars by default are not mass


On 2/7/2012 6:53 PM, Paulo Cesar Telles de Souza wrote:
> 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
> refer.
> What do you think about this option?
> Best,
> Paulo
> Paulo
> 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
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