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>
&gt;<br>
&gt;<br>
&gt; Thanks Justin.<br>
&gt;<br>
&gt; I tried the simulation with Protein_GDP and Water_ions, considering that<br>
&gt; &quot;Water_and_ions&quot; group will include MG. But it didn&#39;t work showing an<br>
&gt; error,saying &quot;One atom not present in the coupling group&quot;. Shall I try<br>
&gt; to include MG in Water_ions group via make_ndx ?<br>
&gt;<br>
<br>
I think the better approach is the one you posted before.<br>
<br>
-Justin<br>
<br>
&gt;<br>
&gt; ----<br>
&gt; Neeru<br>
&gt;<br>
&gt;     neeru sharma wrote:<br>
&gt;      &gt; Dear Gromacs users,<br>
&gt;      &gt;<br>
&gt;      &gt;<br>
&gt;      &gt; I am simulating a system containing a protein with covalently<br>
&gt;     attached<br>
&gt;      &gt; Mg in complex with GDP.<br>
&gt;      &gt;<br>
&gt;      &gt; For nvt equilibration, I have taken protein+Mg+GDP as the single<br>
&gt;     group<br>
&gt;      &gt; and Water+ions as the other. The corresponding block from the<br>
&gt;     .mdp file<br>
&gt;      &gt; is below:<br>
&gt;      &gt;<br>
&gt;      &gt; -- ; Temperature coupling is on<br>
&gt;      &gt; tcoupl      = V-rescale<br>
&gt;      &gt; tc-grps     = Protein_MG_GDP Water_and_ions<br>
&gt;      &gt;<br>
&gt;      &gt;<br>
&gt;      &gt;<br>
&gt;      &gt; Is this coupling method correct, to treat Protein and Mg as different<br>
&gt;      &gt; quantities?<br>
&gt;      &gt;<br>
&gt;<br>
&gt;     You are not treating them differently; they are in a merged group.<br>
&gt;      Note,<br>
&gt;     though, that the default &quot;Water_and_ions&quot; group will include MG, and<br>
&gt;     thus grompp<br>
&gt;     with throw a fatal error.  You&#39;ll have to create a custom group for<br>
&gt;     this one, as<br>
&gt;     well.  Otherwise, the approach seems reasonable to me.<br>
&gt;<br>
&gt;     -Justin<br>
&gt;<br>
&gt;     --<br>
&gt;     ========================================<br>
&gt;<br>
&gt;     Justin A. Lemkul<br>
&gt;     Ph.D. Candidate<br>
&gt;     ICTAS Doctoral Scholar<br>
&gt;     MILES-IGERT Trainee<br>
&gt;     Department of Biochemistry<br>
&gt;     Virginia Tech<br>
&gt;     Blacksburg, VA<br>
&gt;     jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540) 231-9080<br>
&gt;     <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
&gt;<br>
&gt;<br>
</blockquote></div><br>