[gmx-users] how to remove periodicity when using g_rmsd

[Tsjerk Wassenaar]

Hi Tangj Jioawei, Erik.

This is due to periodic boundary conditions. Make sure your molecules
stay together (clustered/nojump) before determining the rmsd. Use
trjconv...

Tsjerk

On 9/27/07, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> My first guess, without knowing how you used g_rms, is that the larde rmsd
> for certain subunits is due to inadequate roto-translational fit prior to
> rmsd-calculation. Does that help? If not, please be more explicit about what
> you aim to do and what you have done.
>
> /Erik
>
>
> 27 sep 2007 kl. 11.29 skrev TANG JIAOWEI:
> Dear all,
> I am studying on a big protein with 16 subunits and when i used g_rmsd to
> one subunit of the protein, the result seems strange that the structure of
> the subunit changes much but it should not.. I searched the mailing list and
> it may be caused by the periodic thing. Could you tell me how to remove the
> periodic thing in detail before i use g_rmsd.
>
> Thank you
>
> Tang jiaowei
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> _______________________________________________
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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