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

Segun Jung dauss75 at gmail.com
Wed Feb 3 23:12:19 CET 2010

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?

Many thanks,

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