[gmx-users] params for g_cluster and g_clustsize

[Dmitri Dubov]

In addition to previous letter (Monday is hard-day!)

It looks like I have known the answers to my questions.

Maybe the reason is that the g_cluster code compared to g_clustsize includes not only single linkage but also other algorithms. So the RMSD feature and smaller default value of -cutoff (which is unusual for single linkage) relate to other algorithms for cluster partitioning. Is it right?

Dmitri

> Dmitri Dubov wrote:
>> Dear gmx'ers,


>> Could you explain me the following points in manuals for g_cluster and 
>> g_clustsize programs?


>> 1) Manual for g_cluster:

>> "single linkage: add a structure to a cluster when its distance to any 
>> element of the cluster is less than cutoff...

>> Other options...

>> -cutoff real 0.1 RMSD cut-off (nm) for two structures to be neighbor"

>> What does "RMSD" mean here?
> Root mean square deviation. Typical for proteins.


>> 2) Manual for g_clustsize:

>> "-cut real 0.35 Largest distance (nm) to be considered in a cluster"

>> Is there any difference between -cut and -cutoff in g_cluster above?

> These are two different programs, unfortunately not sharing any code.


>> Thanks.


>> Dmitri



>> ------------------------------------------------------------------------

>> _______________________________________________
>> 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/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/mailing_lists/users.php





-- 
С уважением,
 Dmitri                          mailto:ddubov at ngs.ru
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090706/cd89a400/attachment.html>