[gmx-users] g_cluster group for output

[Itamar Kass]

Hi all,

I would really appreciate if someone can help me with the "group for
output" option on g_cluster.

When I use g_cluster, it asks me to select two groups. A gourd for fit
and RMSD calculation and a group for output:

Select group for least squares fit and RMSD calculation:
Group     0 (      System) has 205722 elements
Group     1 (     Protein) has 10337 elements
Group     2 (   Protein-H) has  8036 elements
Group     3 (     C-alpha) has  1005 elements

Select group for output:
Group     0 (      System) has 205722 elements
Group     1 (     Protein) has 10337 elements
Group     2 (   Protein-H) has  8036 elements
Group     3 (     C-alpha) has  1005 elements


Know, I have always assumed that g_cluster do a fit and calculate the
RMSD matrix based on the trajectory of the first group, and the second
group is just for control what atoms will be written to the output
file. Recently, however, I did some tests and it seems that the
different groups chosen for "output group" effect not only the atoms
written to the output file, but also the clustering results.

 Can anyone confirm this?

Cheers,
Itamar

-- 


"In theory, there is no difference between theory and practice. But,
in practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at med.monash.edu.au
============================================
the second group?