[gmx-users] position restrain of DNA

[Justin Lemkul]

On 2/21/13 7:35 PM, Mehdi Bagherpour wrote:
> 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?
>
>

As you would any other .itp file; #include it in the topology, within the 
corresponding [moleculetype].

-Justin

>
> 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
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================