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

From: Paulo Cesar Telles de Souza (
Date: Mon Feb 06 2012 - 08:39:02 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.
>> The resulting measurement (RMSD) would be erroneous. Can you elaborate
>> why
>> you'd want this feature available?
>> Best,
>> Chris
>> On Thu, Feb 2, 2012 at 12:19 PM, Paulo Cesar Telles de Souza
>> <> wrote:
>>> Dear colleagues
>>> I'm trying to use the ABF method to get the free energy difference
>>> between two conformation states of a protein. For this, I tried to use
>>> as a reaction coordinate the RMSD of these two conformations, so that
>>> I get a 2D graph (RMSD conformation 1 x RMSD conformation 2, with the
>>> free energy differences given by a color scale). However I have a
>>> question regarding the use of RMSD as a collective variable in the
>>> NAMD program: Can I specify, in the RMSD collective variable,
>>> different atoms for the alignment of protein and to calculate the RMSD
>>> itself. Or must they necessarily be the same in the NAM program?
>>> Thanks
>>> Paulo
>> --
>> Chris Harrison, Ph.D.
>> Theoretical and Computational Biophysics Group
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>> Voice: 773-570-6078
>> Fax: 217-244-6078

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