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

[neeru sharma]

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 ?


----
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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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