[gmx-users] Coupling groups for nvt equilibration

[Justin A. Lemkul]

neeru sharma wrote:
> Dear Gromacs users,
> 
> 
> I am simulating a system containing a protein with covalently attached 
> Mg in complex with GDP.
> 
> For nvt equilibration, I have taken protein+Mg+GDP as the single group 
> and Water+ions as the other. The corresponding block from the .mdp file 
> is below:
> 
> -- ; Temperature coupling is on
> tcoupl      = V-rescale                  
> tc-grps     = Protein_MG_GDP Water_and_ions
> 
> 
> 
> Is this coupling method correct, to treat Protein and Mg as different 
> quantities?
> 

You are not treating them differently; they are in a merged group.  Note, 
though, that the default "Water_and_ions" group will include MG, and thus grompp 
with throw a fatal error.  You'll have to create a custom group for this one, as 
well.  Otherwise, the approach seems reasonable to me.

-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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