[gmx-users] Re: Coupling groups for nvt equilibration

[Justin A. Lemkul]

neeru sharma wrote:
> 
> 
> Thanks Justin.
> 
> I tried the simulation with Protein_GDP and Water_ions, considering that 
> "Water_and_ions" group will include MG. But it didn't work showing an 
> error,saying "One atom not present in the coupling group". Shall I try 
> to include MG in Water_ions group via make_ndx ?
> 

I think the better approach is the one you posted before.

-Justin

> 
> ----
> Neeru
> 
>     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
> 
>     --
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================