[gmx-users] RMSD from the average structure

Justin Lemkul jalemkul at vt.edu
Wed Apr 24 14:17:48 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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