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