[gmx-users] Coupling groups - Thermostat

[Steven Neumann]

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).



>  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>
>
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