[gmx-users] how to analye a single structure (NMR or X-ray) by PCA?

[Tsjerk Wassenaar]

Hi,

Now that particular reference was not a very suitable one for this question :)
The proper reply here is:

There are no collective motions in a single structure, period!

Do some background reading on PCA, and some more on PCA as applied to
MD simulations. There is some information in the manual, there are
plenty of papers and there is a bit of it in the tutorial at
http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html. And there
is indeed a lot said on the mailing list too.

Also note that PCA is not an easy subject.

Cheers,

Tsjerk

On Wed, Mar 24, 2010 at 3:06 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> xi zhao wrote:
>>
>> Dear sir :
>> I want to analye a collective motions of a single structure by PCA , for
>> example, how to choose reference structure using g_covar; how to show its
>> position in 2D-projection (conformational space)?
>> thank you very much!
>
> There have been several discussions on this topic (hint: search the list
> archive), one even in recent days:
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-March/049525.html
>
> Also, read g_covar -h for information about the algorithm.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

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