[gmx-users] g_rms and g_cluster

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 24 14:44:04 CET 2011

shahid nayeem wrote:
> Dear All
> I want to calculate RMSD of one side chain residue from simulation
> trajectory after full backbone alignment as well as translating to
> coincide CA of the residue of interest. Is it possible to do with
> g_rms both backbone alignment as well as translating to coincide CA.

Least-squares fitting is performed on whatever group you choose (i.e. backbone), 
and the calculation group can then be whatever you want.  You can use trjconv to 
do translational fitting, but I don't know that you can force g_rms to always 
align this certain atom and still perform a backbone fit; these two may work 
against one another, even if the difference is small.

> Another clarification is that in gromacs g_cluster how can I use
> greedy algorithm for clustering.

What is a "greedy" algorithm?  The available methods are described in the manual 
and/or g_cluster -h.


> Shahid Nayeem


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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