[gmx-users] RMSD

[Justin A. Lemkul]

On 1/10/10 3:51 AM, leila karami wrote:
> Hi
> I have 2 questions about rmsd calculation:
> 1) why rmsd calculation is done on heavy atoms?

You calculate RMSD on whatever subset of atoms you wish; you are not necessarily 
limited to heavy atoms only.

> 2) what means of mass weighted superposition (rmsd is calculated after
> mass weighted superposition)

Sounds like some background reading is necessary :)

-Justin

>
> Any help will highly appreciated!
>

-- 
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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

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