[gmx-users] position restrain of DNA

[Mehdi Bagherpour]

Thanks Justin

I have any question?

i will use minimization with this restrain.

using genrestr I make min.itp.

how should I use this .itp file in grompp or mdrun?



On Fri, Feb 22, 2013 at 2:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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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