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