[gmx-users] rmsd value discrepancy from g_rms & g_cluster

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 3 23:21:54 CET 2010

Segun Jung wrote:
> Hello there,
> I have used g_rms and g_cluster for RNA structure analysis and noticed 
> that they give me different rmsd values.
> For example, calculating rmsd values using the g_rms gives me a minimum 
> rmsd value of 0.7nm, but using g_cluster
> it gives me the minimum rmsd value of 0.3nm. Both uses the same atom 
> (C3') for the rmsd calculation.
> Would someone clarify this issue?

These tools don't provide a redundant function, from what I understand.  If you 
think that you're somehow using g_cluster to calculate an absolute RMSD, please 
provide the command line you're using.  My understanding of g_cluster (and my 
previous usage of it) suggests that the RMSD is somewhat relative, defining RMSD 
from a cluster member, not a single reference from, for example, the start of 
the simulation (or whatever frame you choose), as is the case with g_rms.

If you're still not convinced, post your command lines and the snippet of the 
relevant output files that are causing you concern.


> Many thanks,
> Segun


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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