[gmx-users] Difference between g_rms and g_rmsdist

[Nawel Mele]

Thanks a lot for your answer.

2013/5/10 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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-- 
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg