[gmx-users] re: g_rms v. g_rmsdist

[Tsjerk Wassenaar]

Hi Gleb,

Apparently I wasn't clear enough. g_rmsdist calculates the average
distance for each pair of atoms over time and then calculates, for
each frame, the deviations from the average distance for each pair of
atoms. Per frame, these deviations are summed and the square root is
taken.
You're right regarding g_rms.

Best,

Tsjerk


On 4/3/07, Gleb Solomentsev <Gleb.Solomentsev at ucd.ie> wrote:
>
>  Hi Tsjerk,
>
> Thanks very much for the response. Just to make sure I understand correctly,
> g_rmsdist calculates an
> average interatom distance value for the reference structure. At a time t, a
> similar average interatom
> distance is calculated and the observed deviation is the difference between
> this value and the average
> interatom distance for the reference structure.
>
> g_rms, at each time t, superimposes as best it can, the current structure
> and the reference structure,
> and calculates the distance deviation between equivalent atoms.
>
> Also, if this is not too complicated of a question, which value is more
> significant? Or does the
>
> Maiorov & Crippen, PROTEINS 22, 273 (1995)
>
> reference go into this.
>
> Thanks again,
> Gleb
>
>
>
> 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 <[EMAIL PROTECTED]> 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
>
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>
>  --
> 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
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
>  Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to [EMAIL PROTECTED] Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>


-- 
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