<br>
<br>
Thanks Justin.<br>
<br>
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 ?<br>
<br>
<br>
----<br>Neeru<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
neeru sharma wrote:<br>
> Dear Gromacs users,<br>
><br>
><br>
> I am simulating a system containing a protein with covalently attached<br>
> Mg in complex with GDP.<br>
><br>
> For nvt equilibration, I have taken protein+Mg+GDP as the single group<br>
> and Water+ions as the other. The corresponding block from the .mdp file<br>
> is below:<br>
><br>
> -- ; Temperature coupling is on<br>
> tcoupl = V-rescale<br>
> tc-grps = Protein_MG_GDP Water_and_ions<br>
><br>
><br>
><br>
> Is this coupling method correct, to treat Protein and Mg as different<br>
> quantities?<br>
><br>
<br>
You are not treating them differently; they are in a merged group. Note,<br>
though, that the default "Water_and_ions" group will include MG, and thus grompp<br>
with throw a fatal error. You'll have to create a custom group for this one, as<br>
well. Otherwise, the approach seems reasonable to me.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br></blockquote></div>
<br>