[gmx-users] g_covar

Yuri Garmay yuri.from.spb at gmail.com
Tue Aug 16 11:45:32 CEST 2011

Hi Tsjerk.

What do you mean with mean? Mean without fitting is a single point.
> Mean only makes sense after aligning. Now there's a nice recursive
> problem:
> 1. Calculate mean to get reference
> 2. Align to reference to calculate mean

I mean the limit of this sequence is mean) Because it is naturally enough to
mean that mean is value that minimizes deviation.
And I know (I learned this a few days ago, in my calculations) that for
flexible molecules such as short peptides it is very another mean that
calculated after first fit. Moreover, if molecule flexible enough, fit to
some frame may be unstable (there may be similar structures that fit in non
similar orientation).

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