[gmx-users] Coupling groups - Thermostat

[Justin A. Lemkul]

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?  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.

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.

-Justin

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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

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