[gmx-users] g_covar

[Tsjerk Wassenaar]

Hi,

> This questuion may be hard. You need rabbi's advice))
> But there are some feature of the reference structure that makes it good or
> bad. It is mean deviation of the atomic coordinates of the fited structures
> from the reference, the best reference minimizes this measure. For a rigid
> structure it is acceptable choice to use first or any other frame, but for a
> flexible it can produce misfit and tangible distortion of the conformations'
> relations.

The reference is used to align the system, not to calculate the
deviations, unless explicitly specified to do so, which usually does
not make sense. I've commented on that on the list on several
occasions. Taking the first frame, or the last or another is all fine.
Just as long as the same reference is used for all trajectories that
are to be compared.

Cheers,

Tsjerk

>
> Yuri.
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands