[gmx-users] Coupling groups - Thermostat

[Steven Neumann]

On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

>
>
> On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> Steven Neumann wrote:
>>
>>> Dear Gmx Users,
>>>  My system includes: ions, water, two tubes made of carbon atoms,
>>> protein.
>>> I would like to run NVT (and then NPT) with position restarined dynamics
>>> of my protein and tubes.
>>> I am wondering whether this approach is good (two coupling groups:
>>> Protein_Tubes and Water_and_ions??
>>>  My thermostat in mdp file:
>>>  Temperature coupling is on
>>>
>>> tcoupl = V-rescale ;
>>>
>>> tc_grps = Protein_Tubes Water_and_ions ; two coupling groups
>>>
>>> tau_t = 0.1 0.1 ; time constant
>>>
>>> ref_t = 298 298 ; reference temperature
>>>
>>> Please, let me know whether this apporach is ok. How can I set tc_grps
>>> when I want to add ligand?
>>>
>>>
>> I don't know a definitive answer here, so I'll throw out some ideas and
>> hopefully stimulate some discussion.  I create tc_grps based on species
>> whose dynamics are intimately linked.  For solvent, that includes water and
>> ions.  Are your protein and tube physically associated?
>
>
> They are not physically associated but I put my protein as close as
> possible to the tube and I want to run position restrained dynamics of my
> tube and first 4 residues of my protein (stimulating attached protein to my
> tube).
>

Will you suggest attaching my protein directly to my tube in this case?

>
>
>
>>  If not, it doesn't make sense to me to couple them together. In reality,
>> no group should ever be coupled independently, but limitations in
>> thermostats make it necessary.
>>
>
> Would you suggest specifing 3 groups in this case: Protein, Tube,
> Water_and_ions ?
>
>>
>> Regarding the ligand, where is it?  Floating around in solvent, bound to
>> the protein, or in the tube?  The answer to that question motivates how you
>> treat it.
>>
>> With this simulation there is no ligand. My next simulation will be with
> 10-20 ligands placed randomly around the protein. I want to assess the
> influence of lmy ligands to the stability of the protein, that is why I
> need a comparison (in water only and in water with ligands).
> I am wondering how to specify coupling groups in this case.
>
> Steven
>
>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120110/acfccdd9/attachment.html>