[gmx-users] RMSD of the same protein in different solvent boxes

[Tsjerk Wassenaar]

Hi Afonso,

Try to first extract the protein from both simulations using trjconv,
or even the backbone trajectories.

Cheers,

Tsjerk

On 2/5/07, Afonso Duarte <duartenl at yahoo.com.br> wrote:
> Hi to All,
>
> I have some simulations of the same protein in different solvents, with
> different number of atoms for each (different solvent number of atoms).
> I would like to calculate a rmsd matrix to compar the backbone of the
> different sims.
>
> I have tried g_rms with the -f2 option to include the second trajectory,
> however it finishes with a fatal error because teh number of total atoms is
> different in both trajectories.
>
> Does anybody know how to solve this question? Is it possible to produce the
> rmsd matrix in a different way?
>
> Thanks in advance
>
> Afonso
>
>
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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