From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Feb 02 2012 - 15:40:47 CST
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 <charris5_at_gmail.com> 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
> <paulocts_at_gmail.com> 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
>
> char_at_ks.uiuc.edu Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
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