[gmx-users] on the "tc-grps = Protein Non-Protein ; two coupling groups" in the on-line tutorial

[Justin A. Lemkul]

Acoot Brett wrote:
> Dear All,
>  
> In the on-line tutorial of *Justin Lemkul 
> *(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html) 
> for both lysozyme and the umbrella sampling, in the npt.mdp, there is 
> "tc-grps         = Protein Non-Protein   ; two coupling groups".
>  
> In the system of lysozyme, the system contains protein, SOL and CL-. In 
> the system of umbrella sampling, the system contains protein, SOL, Na+ 
> and CL-.
>  
> Correspondingly will you please explain to me how "Non-Protein" group 
> should be defined?
>  

The "Non-protein" group is one that Gromacs generates automatically:

http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups

As the name implies, it includes everything that is not protein.

-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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