[gmx-users] RMSD between two groups

[Mohsen Ramezanpour]

Hi,

How about using g_dist and using an index file?!

Cheers
Mohsen

On Mon, Mar 23, 2015 at 6:50 PM, leila salimi <leilasalimi at gmail.com> wrote:

> Dear all,
>
> I have a question regarding to analyse the trajectory that I have. I am
> studying the interaction of peptide at interfaces, e.g Oxygen of
> carboxylate group of side chains with Cations at the interface!
> I would like to calculate the distance between Oxygen of carboxylate group
> of side chains and specific ions of solid at the interface! I used gmx rms
> but I think I did wrong calculation.
>
> Could you suggest me which tool can give the overview of distance
> fluctuation between two group of atoms?
>
> Regards,
> Leila
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