Justin,<br><br>I tried to use an index file with atom numbers of the water molecules in the required volume.<br><br>But when I try to ionize the box, I get this error:<br> <br>Fatal error:<br>The solvent group SOL is not continuous: index[717]=21689, index[718]=21696<br>
<br>This makes sense, but is there a way get around this?<br><br>SR<br><br><div class="gmail_quote">On Thu, Mar 25, 2010 at 5:17 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Smiruthi Ramasubramanian wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
I am simulating an ion channel and require help placing a concentration of ions at one side of the box (below the membrane).<br>
<br>
</blockquote>
<br></div>
"Sidedness" is irrelevant in a periodic system; the water layers are continuous with PBC.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
SETUP: membrane + embedded protein in the center of the cube.<br>
<br>
I tried to generate a smaller cube (of the required volume below the cube), solvate, add ions and then /cat/ with the *.gro file of my system before solvating. But when I solvate the system with ions, the ions are removed.<br>
<br>
Any suggestions as to how to handle this problem?<br>
<br>
</blockquote>
<br></div>
I don't fully understand what you tried to do, but it should be possible to solvate the unit cell normally, create an index group for the waters on one "side" of the membrane, and pass this index file to the -n flag of genion. Creating the index file may involve writing your own script to collect the atom numbers. As far as I am aware, make_ndx cannot, for example, select all water molecules below/above some z-coordinate, which would be required for your situation.<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>
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