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.
-Justin
Many thanks,
Segun
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
