[gmx-users] position restrain of DNA

[Justin Lemkul]

On 2/22/13 4:37 AM, Mehdi Bagherpour wrote:
> Tanks Justin
>
> Should I use from 'define = -DPOSRES'  in mdp file?
>

Use whatever #ifdef construct makes sense.  The -DPOSRES uses the default 
posre.itp written by pdb2gmx, which restrains all heavy atoms.  Unless you've 
modified the topology, that approach will not use your special restraint file.

-Justin

>
> 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
>>>>
>>>> --
>>>> ==============================****==========
>>>>
>>>>
>>>> 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://vt.edu/Pages/Personal/justin>
>>>> <h**ttp://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<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

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