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<div class="gmail_quote">On Fri, Jan 6, 2012 at 4:04 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br><br>Steven Neumann wrote:
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<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br><br>On Fri, Jan 6, 2012 at 3:48 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Steven Neumann wrote:<br><br> Dear Gmx Users,<br> I am setting up the simulation of a protein attached to the<br> half of a nanotube. I set up my system and formed my box and<br> solvated it in TIP3P water. Water molecules obviously were also<br>
placed below the part of a nanotube where I do not want them to<br> be. Is there any command which will solvate my system below the<br> surface of the nanotube? Or maybe is there any command or a<br> software that will allow me to remove those unwanted water<br>
molecules? I have aroun 26000 water molecules in my system and<br> around 5000 below my nanoutube so with editor it could take<br> ages. Any suggestions?<br> <br><br> You can use g_select to use geometric criteria, i.e. coordinate<br>
value > some number such that only water molecules above a certain<br> point are kept. Then use trjconv with the index file g_select gives<br> you and you have your cleaned up system.<br><br> -Justin<br><br>Thank you Justin. That makes sense. Can you please write me which option of g_select will do this? How to see the help for each option?<br>
<br></blockquote><br></div></div>Try:<br><br>g_select -select "help all"<br><br>Also note that similar procedures to what you want to do are described in the list archive.
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<div><br><br>-Justin</div></div></blockquote>
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<div>Thank you. I would appreciate a link of similar problem as I cannot find it at all. Thank you.</div>
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<div>Steven</div></div>