[gmx-users] g_rms warning

[Tsjerk Wassenaar]

Hi Carla,

You'll have to use index groups to extract a trajectory and reference
that correspond. If you have those you can get on with the RMSD.

Cheers,

Tsjerk

On Mon, Mar 8, 2010 at 11:44 AM, Carla Jamous <carlajamous at gmail.com> wrote:
> Hi everyone, please I just need a precision:
>
> I need to calculate the RMSD of a trajectory by comparing it to a reference
> structure that doesn't have the same number of atoms.
> Gromacs is calculating the RMSD, but meanwhile it generates this
> warning:"topology has 4839 atoms, whereas trajectory has 4834"
>
> Does it really affect the result of my RMSD or can I ignore it?
>
> Thanks
> Carla
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist