[gmx-users] position restrain of DNA

[Mehdi Bagherpour]

Tanks Justin

Should I use from 'define = -DPOSRES'  in mdp file?


On Fri, Feb 22, 2013 at 4:13 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

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