[gmx-users] position restrain of DNA

Justin Lemkul jalemkul at vt.edu
Fri Feb 22 00:11:10 CET 2013

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 



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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