[gmx-users] RMDS calculation

[vferrario at units.it]

Sorry but the help does not help me... In anycase, the help of  
g_rmsdist say: "g_rmsdist computes the root mean square deviation of  
atom distances, which
has the advantage that no fit is needed like in standard RMS deviation as
computed by g_rms..."; so no fit is needed, for me it means that there  
is no superimposition... Can you explain me where I'm wrong?

Valerio

Tsjerk Wassenaar <tsjerkw at gmail.com> ha scritto:

> Hi Valerio,
>
> Check the help for both tools. That explains it all.
> Oh, and you're not correct ;)
>
> Cheers,
>
> Tsjerk
>
> On Mon, Dec 5, 2011 at 4:42 PM,  <vferrario at units.it> wrote:
>> Dear all,
>>
>> I need to calculate the RMSD of a protein during time. So that I've
>> calculated the trajectory; for the calculation which tool should I use?
>> g_rms or g_rmsdist ? Which is the difference between these two tools? If I'm
>> right the main difference is that with g_rms the structure at the time t is
>> superimposed to the reference structure before calculate the RMSD, while
>> with g_rmsdist the RMSD is calculated without any superimposition, am I
>> correct?
>>
>> Valerio
>>
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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