[gmx-users] g_rms v. g_rmsdist

[Tsjerk Wassenaar]

Hi Gleb,

g_rmsdist calculates a matrix of interatomic distances, averages these
and calculates the average deviation from the average. g_rms
superimposes two structures (superimposes the averages) and calculates
the average deviation over the pairs of equal atoms in the structures.

Hope I am clear enough...

Best,

Tsjerk

On 3/15/07, Gleb Solomentsev <Gleb.Solomentsev at ucd.ie> wrote:
>
>  Hello,
>
>  I am trying to figure out what the difference between these two
> applications is. The calculation is of the RMSD for a protein unfolding
> trajectory and I get different results with g_rms and g_rmsdist. I have
> looked at the manual and all I can find is that:
>
>  "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."
>
>  What fit is this referring to and would this be the source of my
> differences?
>
>  I am getting larger RMSD values using g_rms.
>
>  Thanks,
>  Gleb
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623