[gmx-users] RMSD from the average structure

[Justin Lemkul]

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

-- 
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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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