On 4/24/13 3:06 AM, bipin singh wrote:
Hi all,
Please let me know whether this is the right way to calculate RMSD from the
average structure from a simulation:
g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
average.pdb: is the pdb file produced using -ox option of g_rmsf.
You can calculate RMSD with respect to whatever structure you like, but the
interpretation and justification for doing so are up to you.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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