Thanks Justin.<br><br>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.<br><br>Thanks again...<br>
<br>____<br>Neeru<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">
<br>
neeru sharma wrote:<br>
><br>
><br>
> Thanks Justin.<br>
><br>
> I tried the simulation with Protein_GDP and Water_ions, considering that<br>
> "Water_and_ions" group will include MG. But it didn't work showing an<br>
> error,saying "One atom not present in the coupling group". Shall I try<br>
> to include MG in Water_ions group via make_ndx ?<br>
><br>
<br>
I think the better approach is the one you posted before.<br>
<br>
-Justin<br>
<br>
><br>
> ----<br>
> Neeru<br>
><br>
> neeru sharma wrote:<br>
> > Dear Gromacs users,<br>
> ><br>
> ><br>
> > I am simulating a system containing a protein with covalently<br>
> attached<br>
> > Mg in complex with GDP.<br>
> ><br>
> > For nvt equilibration, I have taken protein+Mg+GDP as the single<br>
> group<br>
> > and Water+ions as the other. The corresponding block from the<br>
> .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.<br>
> Note,<br>
> though, that the default "Water_and_ions" group will include MG, and<br>
> thus grompp<br>
> with throw a fatal error. You'll have to create a custom group for<br>
> 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> <<a href="http://vt.edu" target="_blank">http://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>
><br>
><br>
</blockquote></div><br>