[gmx-users] RMSD question

[Tsjerk Wassenaar]

Hi Teresa,

You probably want to try clustering, and then check the percentage of
bound/unbound structures in the clusters you get. Just the RMSD won't tell
you much.

Cheers,

Tsjerk

On Wed, Jun 8, 2016 at 11:30 AM, ingram <ingram at fhi-berlin.mpg.de> wrote:

> Dear GROMACS community,
>
> I am trying to identify the number of unique peptide structures on the
> surface of a slab. If I simply calculate the RMSD between the protein atoms
> in each frame of the trajectory this tells me nothing about how these
> structures compare on the surface as the constraint of the surface will not
> be taken into account. Can anyone suggest what I should use as a reference
> structure and what I structures I should compare when calculating the RMSD
>
>
> BEst
>
> Teresa
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-- 
Tsjerk A. Wassenaar, Ph.D.