[gmx-users] Difference between g_rms and g_rmsdist

[Justin Lemkul]

On 5/10/13 4:24 AM, Nawel Mele wrote:
> Hi,
>
> I am trying to understand what is the difference between g_rms and
> g_rmsdist commands.
> I have looked at the manual and all I can find is that:
>
> *g_rms*: The root mean square deviation (RM SD) of certain atoms in a
> molecule with respect to a reference
> structure can be calculated with the program g_rms by least-square fitting
> the structure to the reference
> structure (t2 = 0) and subsequently calculating the RMSD
> *
> g_rmsdist*: Alternatively the RMSD can be computed using a fit-free method
> with the program g_rmsdist
>
>
>
> What fit is this referring to ?
>

RMSD is normally calculated after a least-squares fit to eliminate the influence 
of global rotations and translations that would otherwise result in spuriously 
high RMSD values.  In the case of g_rmsdist, no fitting is done, and has 
different applications (explained in the help description).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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