<div>Thank you. Should I also copy and paste coordinates of my ions or just my protein?</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Tue, Jan 10, 2012 at 11:03 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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">On 10/01/2012 9:54 PM, 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 my simulations of carbon tube with protein. I solvated my system, added ions and I would like to run EM of my system. My carbons of the tube in MD will be restrained. In this case should I run EM of my protein in water (and with ions) separately and the copy coordinates and then process with NVT and NPT or run EM with restrained nanotubes of my system directly?<br>
</blockquote><br></div>The former is less likely to have problems.<span class="HOEnZb"><font color="#888888"><br><br>Mark<br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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</font></span></blockquote></div><br>