[gmx-users] position restrain of DNA

[Justin Lemkul]

On 2/21/13 6:09 PM, Mehdi Bagherpour wrote:
> I am using Gromacs software for DNA simulation. Specially in my project I
> need to fix two ends base pairs of DNA,The DNA that I want to simulate has
> 12 sequence shown bellow
>
> 5-- *C*GCAAAAAACG*C* --3
> 3-- *G*CGTTTTTTGC*G*  --5
>
> I dont know how I can use from position restraint in gromacs.
>
> would you please help me to solve this problem?
>

Use genrestr with an index group specifying whatever it is that you want to 
restrain.

-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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