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

[Justin A. Lemkul]

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

========================================