[gmx-users] g_covar

[Tsjerk Wassenaar]

Hey Yuri,

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
(http://xkcd.com/754/)

But think about it... aligning to some reference is good enough to fix
the mean and the covariance matrix. :)

Cheers,

Tsjerk

On Tue, Aug 16, 2011 at 11:16 AM, Yuri Garmay <yuri.from.spb at gmail.com> wrote:
> I know, but the best reference is "mean". And it is another mean that
> calculated after fit at some frame.
>
> 2011/8/16 Tsjerk Wassenaar <tsjerkw at gmail.com>
>>
>> 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.
>> >
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>>
>>
>>
>> --
>> 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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
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