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

[neeru sharma]

Thanks Justin.

I have tried both ways now and considering Protein_MG_GDP and Water_ions
groups, it is running without any error but Protein_GDP and MG_Water_ions
is failing with an error message.

Thanks again...

____
Neeru

>
> 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
> >
> >
>
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